Skosmos Server error

[Sandor Kopacsi]

Dear Osma,

I have installed JenaFuseki and Skosmos on Centos 6.6 according to the installation guid , and updated Java version to jre-1.8.0.

I could start Skosmos fine, but trying to open the built-in vocabularies (YSA or YSO), I get the server error message 500.

What can be wrong?

Thanks in advance!

Sandor

 

[Osma Suominen]

On 04/11/15 16:30, Sandor Kopacsi wrote:

> I have installed JenaFuseki and Skosmos on Centos 6.6 according to the
> installation guid , and updated Java version to jre-1.8.0.
> I could start Skosmos fine, but trying to open the built-in vocabularies
> (YSA or YSO), I get the server error message 500.
> What can be wrong?

Hi Sandor!

You really need to tell more details.

What is the specific error message you get?

Is there anything in the Apache error log?

What kind of configuration (config.inc and vocabularies.ttl) do you use?

-Osma

--
Osma Suominen
D.Sc. (Tech), Information Systems Specialist
National Library of Finland
P.O. Box 26 (Kaikukatu 4)
00014 HELSINGIN YLIOPISTO
Tel. +358 50 3199529
osma.s...@helsinki.fi
http://www.nationallibrary.fi

[Sandor Kopacsi]

Dear Osma,

After starting Fuseki (from its directory using the command ./fuseki-server --update --mem /ds) and Skosmos (by typing in the browser http://skosmos.phaidra.org) , and then clicking on YSA or YSO on the main screen of Skosmos, I got the error message 500, and the details are as follow:

"The website encountered an error while retrieving http://skosmos.phaidra.org/ysa/en/. It may be down for maintenance or configured incorrectly."

(Skosmos is running on a virtual host, named skosmos.phaidra.org. The document root is  /var/www/skosmos, where Skosmos was installed.)

I use the default config.inc and vocabularies.ttl (renamed  the *.dist files), and I modified config.inc like this:

define("DEFAULT_ENDPOINT", "http://skosmos.phaidra.org:3030/ds/sparql");

Apache is configured so at the moment, that it doesn't create error log file.

What should I modify?

Thank you very much for your help.

Best Regards,

Sandor

[Osma Suominen]

Dear Sandor,

Thank you for the details!

The error message is unfortunately just a generic error displayed by the
browser, it doesn't really tell what's wrong. I suspect Apache and/or
Skosmos would be able give a more informative error message, but it is
not displayed by your browser.

You should really enable the Apache error log and see what ends up
there. It is very useful to have in any case.

As an alternative you could try another browser. For example
Chrome/Chromium doesn't block server-side error messages AFAIK. Or you
could configure IE or Firefox to not display "friendly" error messages,
which hide the original error (thanks browser guys, really helpful
behavior!), see here:
https://support.microsoft.com/en-us/kb/294807
http://www.thinklemon.com/weblog/2005/06/22/turning-off-the-friendly-http-error-messages-in-firefox/

Some guesses as to what could be wrong:
- have you installed all the dependencies with Composer?
- maybe your server/Apache doesn't have access to the
http://api.dev.finto.fi/sparql endpoint? For example firewall rules or
SELinux could block it.

-Osma

05.11.2015, 22:49, Sandor Kopacsi kirjoitti:
> Dear Osma,
>
> After starting Fuseki (from its directory using the command
> ./fuseki-server --update --mem /ds) and Skosmos (by typing in the
> browser http://skosmos.phaidra.org) , and then clicking on YSA or YSO on
> the main screen of Skosmos, I got the error message 500, and the details
> are as follow:
> "The website encountered an error while retrieving

> *http://skosmos.phaidra.org/ysa/en/*. It may be down for maintenance or
> configured incorrectly."
> (Skosmos is running on a virtual host, named *skosmos.phaidra.org. *The

> osma.s...@helsinki.fi <javascript:>
> http://www.nationallibrary.fi
>
> --
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> For more options, visit https://groups.google.com/d/optout.

[Sandor Kopacsi]

Dear Oma,

thank you very much  for your answer.

I have created the error log file, and from it it turned out, that the problem was the lack of date.timezone setting:

"PHP Fatal error:  Uncaught exception 'Exception' with message 'DateTime::__construct(): It is not safe to rely on the system's timezone settings. You are *required* to use the date.timezone setting or the date_default_timezone_set() function."

(I know, that there was a warning in installation step 4 to "make sure you have the date.timezone setting configured, otherwise you may get errors displaying date values", but I skipped this step, because I thought that it can cause just displaying problems. Sorry.)

Now I have set the date.timezone value, and now Skosmos works with YSO and YSA fine! :-)

I tried again setting the getty's tgn vocabulary to Skosmos, using the suggestion from a Getty's forum:

 

"The endpoint is http://vocab.getty.edu/sparql, and the 3 schemes are http://vocab.getty.edu/aat, http://vocab.getty.edu/tgn, http://vocab.getty.edu/ulan.

This is documented at http://vocab.getty.edu/doc/#Descriptive_Entities (and following sections) and available in machine-readable fashion in VOID.
Please read http://vocab.getty.edu/doc/#Top_Concepts: we don't have skos:topConceptOf and skos:hasTopConcept (for the reasons described there), 
and instead use iso:ThesaurusArray with http://vocab.getty.edu/doc/#Standard_Hierarchical_Relations and http://vocab.getty.edu/doc/#GVP_Hierarchical_Relations.
If Skosmos relies on skos:hasTopConcept and is limited to concepts, that may be a problem."

I set the for getty's tgn in the vocabularies.ttl like this:

@ prefix >iso: http://vocab.getty.edu/doc/#Standard_Hierarchical_Relations>.

:tgno a skosmos:Vocabulary, void:Dataset ;

        dc:title "TGNO - Getty Thesaurus of Geographic Names - online"@en ;

        dc:subject :cat_general ;

        void:uriSpace "http://vocab.getty.edu/tgn";

        skosmos:language "en";

        skosmos:showTopConcepts "false";

        iso:ThesaurusArray "true";

        skosmos:loadExternalResources "true";

        skosmos:fullAlphabeticalIndex "true";

        skosmos:groupClass isothes:ConceptGroup ;

        skosmos:arrayClass isothes:ThesaurusArray ;

        void:sparqlEndpoint <http://vocab.getty.edu/sparql> .

I have received the same server error 500, and now I found this entry in the error log file:

[error] [client 131.130.2.250] PHP Fatal error:  Uncaught exception 'EasyRdf_Exception' with message 'HTTP request for SPARQL query failed: <html><head><title>Apache Tomcat/7.0.42 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 404 - </h1><HR size="1" noshade="noshade"><p><b>type</b> Status report</p><p><b>message</b> <u></u></p><p><b>description</b> <u>The requested resource is not available.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.42</h in /var/www/skosmos/vendor/twig/twig/lib/Twig/Template.php on line 279, referer: http://skosmos.phaidra.org/en/?clang=

What do you suggest, how to go on?

Thanks a lot.

Best Regards,

Sandor

> <mailto:skosmos-users+unsub...@googlegroups.com>.

[Osma Suominen]

Dear Sandor,

Please find my comments below.

06.11.2015, 12:43, Sandor Kopacsi kirjoitti:
> (I know, that there was a warning in installation step 4 to "make sure
> you have the date.timezone setting configured, otherwise you may get
> errors displaying date values", but I skipped this step, because I
> thought that it can cause just displaying problems. Sorry.)

Good that you found the issue! I changed the wording of that section to
make it more explicit.

> Now I have set the date.timezone value, and now Skosmos works with YSO
> and YSA fine! :-)

Excellent!

> I tried again setting the getty's tgn vocabulary to Skosmos, using the
> suggestion from a Getty's forum:
> "The endpoint is http://vocab.getty.edu/sparql, and the 3 schemes are
> http://vocab.getty.edu/aat, http://vocab.getty.edu/tgn,
> http://vocab.getty.edu/ulan.
> This is documented at http://vocab.getty.edu/doc/#Descriptive_Entities
> <http://vocab.getty.edu/doc/#Descriptive_Entities> (and following
> sections) and available in machine-readable fashion in VOID.
> Please read http://vocab.getty.edu/doc/#Top_Concepts
> <http://vocab.getty.edu/doc/#Top_Concepts>: we don't have
> skos:topConceptOf and skos:hasTopConcept (for the reasons described there),
> and instead use iso:ThesaurusArray with
> http://vocab.getty.edu/doc/#Standard_Hierarchical_Relations

> <http://www.google.com/url?q=http%3A%2F%2Fvocab.getty.edu%2Fdoc%2F%23Standard_Hierarchical_Relations&sa=D&sntz=1&usg=AFQjCNHj79uihAqdh4NUnSh8v9tcsVPhJw> and
> http://vocab.getty.edu/doc/#GVP_Hierarchical_Relations
> <http://vocab.getty.edu/doc/#GVP_Hierarchical_Relations>.

> If Skosmos relies on skos:hasTopConcept and is limited to concepts, that
> may be a problem."

Yes, Skosmos does rely on hasTopConcept but it is only necessary if you
enable the showTopConcepts setting.

> I set the for getty's tgn in the vocabularies.ttl like this:
>
> @ prefix >iso: http://vocab.getty.edu/doc/#Standard_Hierarchical_Relations>.

That looks wrong...there is extra spacing, the brackets are in the wrong
places, and even the namespace is not what I'd expect.
I don't think you need this prefix declaration anyway; below you use
isothes: which should already be defined in the example vocabularies.ttl
file.

> :tgno a skosmos:Vocabulary, void:Dataset ;
> dc:title "TGNO - Getty Thesaurus of Geographic Names - online"@en ;
> dc:subject :cat_general ;
> void:uriSpace "http://vocab.getty.edu/tgn";
> skosmos:language "en";
> skosmos:showTopConcepts "false";
> iso:ThesaurusArray "true";
> skosmos:loadExternalResources "true";
> skosmos:fullAlphabeticalIndex "true";
> skosmos:groupClass isothes:ConceptGroup ;
> skosmos:arrayClass isothes:ThesaurusArray ;
> void:sparqlEndpoint <http://vocab.getty.edu/sparql> .

Looks about right, except for the uriSpace setting, which I think needs
an extra slash at the end.

> I have received the same server error 500, and now I found this entry in
> the error log file:
> [error] [client 131.130.2.250] PHP Fatal error: Uncaught exception
> 'EasyRdf_Exception' with message 'HTTP request for SPARQL query failed:
> <html><head><title>Apache Tomcat/7.0.42 - Error
> report</title><style><!--H1
> {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;}
> H2
> {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;}
> H3
> {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;}
> BODY
> {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B
> {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;}
> P
> {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A
> {color : black;}A.name {color : black;}HR {color : #525D76;}--></style>
> </head><body><h1>HTTP Status 404 - </h1><HR size="1"
> noshade="noshade"><p><b>type</b> Status report</p><p><b>message</b>
> <u></u></p><p><b>description</b> <u>The requested resource is not
> available.</u></p><HR size="1" noshade="noshade"><h3>Apache
> Tomcat/7.0.42</h in
> /var/www/skosmos/vendor/twig/twig/lib/Twig/Template.php on line 279,
> referer: http://skosmos.phaidra.org/en/?clang=

The Getty SPARQL endpoint is not responding in the right way. There
seems to be some incompatibility between Skosmos (in practice, the
EasyRdf library which is used to perform SPARQL queries) and the Getty
SPARQL endpoint. I don't know the reason for this, it would need more
investigation.

> What do you suggest, how to go on?

I think you'd be better off setting up your own Fuseki SPARQL endpoint,
with the jena-text index. Even if you could access the Getty SPARQL
endpoint, it would most likely be extremely slow to use it with Skosmos,
since it doesn't have a text index that Skosmos could use.

https://github.com/NatLibFi/Skosmos/wiki/InstallFusekiJenaText

I suggest you set up Fuseki (with jena-text) and then put some much
smaller and simpler SKOS dataset there for testing. For example, the STW
Thesaurus and/or UNESCO Thesaurus would work for this. Once you get
these working, you can then try one of the Getty vocabularies. Though as
I've said before, I think it's unlikely that the Getty vocabularies
would work well in Skosmos due to their very large size. However, using
a small subset could still work.

We have both the STW and UNESCO thesauri configured on the
skosmos.dev.finto.fi demo site. To see how they are configured, you can
take a look at the configuration file:
http://skosmos.dev.finto.fi/vocabularies.ttl

The STW and UNESCO thesauri are available for download from their
respective home pages:
http://zbw.eu/stw/version/latest/about
http://skos.um.es/unescothes/

-Osma

--
Osma Suominen
D.Sc. (Tech), Information Systems Specialist
National Library of Finland
P.O. Box 26 (Kaikukatu 4)
00014 HELSINGIN YLIOPISTO
Tel. +358 50 3199529
osma.s...@helsinki.fi

http://www.nationallibrary.fi

[Sandor Kopacsi]

Dear Osma,

thank you for your useful help again.

I tried UNESCO, STW as well as AGROVOC thesauri, but I found that with

dc:subject: cat_culture

dc:subject: cat_science

dc:subject: cat_society

Skosmos even does not display their link in the opening page.

If I change them to 

dc:subject: cat_general

then UNESCO and STW work fine from the remote SPRAQL endpoint, but AGROVOC requires rather long time to load the items. Is it normal?

According to your suggestion I have set the the jena-text configuration to Fuseki, but some questions occurred:

If I run  Fuseki with ./fuseki-server --config jena-text-config.ttl then it completely substitutes the previously used ./fuseki-server --mem /ds command? I did not find the --mem option. Is it not required?

What is the difference, if I set and use the FUSEKI_CONF= environment variable?

Have you find the reason why the Getty SPARQL endpoint is not responding in the right way?

Now I try to download the STW and UNESCO thesauri, and try it locally, but before that a (maybe silly question): 

Do I have to run Fuseki (with or witout jena-text extension) even when I use the remote SPARQL endpoint of a data set?

Thank very much you!

Best Regards,

Sandor

[Osma Suominen]

Hi Sandor!

On 11/11/15 13:21, Sandor Kopacsi wrote:
> Dear Osma,
> thank you for your useful help again.
> I tried UNESCO, STW as well as AGROVOC thesauri, but I found that with
>
> dc:subject: cat_culture
> dc:subject: cat_science
> dc:subject: cat_society
>
> Skosmos even does not display their link in the opening page.

The categories have to be defined in the same vocabularies.ttl file. For
the skosmos.dev.finto.fi demo site, we have defined six categories
(loosely based on the UDC top level categories). You need to copy the
category definitions to your file as well, or change everything to
cat_general as you already did.

> If I change them to
>
> dc:subject: cat_general
>
> then UNESCO and STW work fine from the remote SPRAQL endpoint, but
> AGROVOC requires rather long time to load the items. Is it normal?

AGROVOC is a bit slow to load the first time because it has so many
labels. It should be cached by Varnish (which is installed in front of
our endpoint) and load quicker after that.

> According to your suggestion I have set the the jena-text configuration
> to Fuseki, but some questions occurred:
>
> If I run Fuseki with ./fuseki-server --config jena-text-config.ttl then
> it completely substitutes the previously used ./fuseki-server --mem /ds
> command? I did not find the --mem option. Is it not required?

The --mem option is a shorthand for running Fuseki without a
configuration file. (--file is similar too)

You need a configuration file to use jena-text so you must use
./fuseki-server --config jena-text-config.ttl

> What is the difference, if I set and use the FUSEKI_CONF= environment
> variable?

If you use the init script (/etc/init.d/fuseki), then the environment
variable is used to set the configuration file. But if you just run
Fuseki from the command line, you need to use the --conf option.

> Have you find the reason why the Getty SPARQL endpoint is not responding
> in the right way?

No, I haven't looked.

> Now I try to download the STW and UNESCO thesauri, and try it locally,
> but before that a (maybe silly question):
> Do I have to run Fuseki (with or witout jena-text extension) even when I
> use the remote SPARQL endpoint of a data set?

No. Either you use a remote SPARQL endpoint, or you use Fuseki locally.
You could of course have one vocabulary from a remote endpoint and
another from a local Fuseki, but generally you don't need both.

In any case I suggest you set up a local Fuseki with jena-text and load
that with UNESCO or STW. When you get that working, you can try loading
the Getty vocabularies instead.

[Sandor Kopacsi]

Dear Osma,

I have configured and started Fuseki using text index, and uploaded unescothes.rdf with success (75193 Triples have been loaded).

I have set a section for this vocabulary in the vocabularies.ttl as follow:

:unl a skosmos:Vocabulary, void:Dataset ;

        dc:title "UNESCO Thesaurus - local"@en ;

        skosmos:shortName "UNESCO";

        dc:subject :cat_general ;

        void:uriSpace "http://skos.um.es/unescothes/";

        skosmos:language "en", "es", "fr", "ru";

        skosmos:defaultLanguage "en";

        skosmos:showTopConcepts "true";

        skosmos:groupClass isothes:ConceptGroup ;

        void:sparqlEndpoint <http://skosmos.phaidra.org:3030/ds> ;

        skosmos:sparqlGraph <http://skos.um.es/unescothes/> .

Selecting this item form Skosmos, I got Server error 500 again, and in the error log file states:

 PHP Fatal error:  Uncaught exception 'EasyRdf_Exception' with message 'HTTP request for SPARQL query failed: Error 404: Not Found\n\n\nFuseki - version 1.3.0 (Build date: 2015-07-25T17:11:28+0000)\n' in /var/www/skosmos/vendor/easyrdf/easyrdf/lib/EasyRdf/Sparql/Client.php:290\nStack trace:\n#0 /var/www/skosmos/vendor/easyrdf/easyrdf/lib/EasyRdf/Sparql/Client.php(120): EasyRdf_Sparql_Client->request('query', 'SELECT ?cs ?lab...')\n#1 /var/www/skosmos/model/sparql/GenericSparql.php(398): EasyRdf_Sparql_Client->query('SELECT ?cs ?lab...')\n#2 /var/www/skosmos/model/Vocabulary.php(309): GenericSparql->queryConceptSchemes('en')\n#3 /var/www/skosmos/model/Vocabulary.php(324): Vocabulary->getConceptSchemes()\n#4 /var/www/skosmos/model/Vocabulary.php(251): Vocabulary->getDefaultConceptScheme()\n#5 [internal function]: Vocabulary->getInfo('en')\n#6 /var/www/skosmos/vendor/twig/twig/lib/Twig/Template.php(437): call_user_func_array(Array, Array)\n#7 /tmp/skosmos-template-cache/d5/52/a588782056aa2d97ee830f93210b.php(31): Twig_Template->getAttribute(Ob in /var/www/skosmos/vendor/twig/twig/lib/Twig/Template.php on line 279, referer: http://skosmos.phaidra.org/en/?clang=

If I modify the sparqlEndpoint setting like this:

void:sparqlEndpoint <http://skosmos.phaidra.org:3030> ; 

(that I don't think that is good), then I don't get the server error, but a message in the Alphabetical Tab of Skosmos' page:

The vocabulary does not contain terms beginning with "A"!

and in the Vocabulary information all Term counts by language is zero!

If I change the sparqlEndpoint to remote one like this:

void:sparqlEndpoint <http://api.skosmos.dev.finto.fi/sparql> ;

then everything works fine. 

What can be wrong?

Thanks in advance for your help!

Best Regards,

Sandor

[Osma Suominen]

Hi Sandor!

I assume Fuseki is running on the same machine as Skosmos? So it's
probably accessible as "localhost". In any case, the endpoint URI should
end with "/ds/sparql".

What if you set
void:sparqlEndpoint <http://localhost:3030/ds/sparql>
or
void:sparqlEndpoint <http://skosmos.phaidra.org:3030/ds/sparql>

Hope this helps,
-Osma

> the skosmos.dev.finto.fi <http://skosmos.dev.finto.fi> demo site, we

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> http://www.nationallibrary.fi
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[Sandor Kopacsi]

Dear Osma,

Thank you for your quick response!

Skosmos and  Fuseki running on the same remote CentOS machine, that I access from Windows through SSH and using Skosmos and Fuseki through a web browser on the address http://skosmos.phaidra.org and http://skosmos.phaidra.org:3030.

I tried with both http://skosmos.phaidra.org:3030/ds/sparql  and http://localhost:3030/ds/sparql and I still get the message  'The vocabulary does not contain terms beginning with "A"!' in the Alphabetical Tab of Skosmos' page, and in the Vocabulary information panel all 'Term counts by language' are zero!

Can it be that Fuseki doesn't store the data set? 

I am not very familiar with SPARQL, but I have tried some SPARQL queries on the apparently successfully uploaded unescothes.rdf data set, like 

PREFIX dcterms: <http://purl.org/dc/terms/>

PREFIX unescothes: <http://skos.um.es/unescothes/> 

SELECT ?creator

WHERE

{ 

 unescothes:CS000 dcterms:creator ?creator.

}

But I never get any content, just like this:

-----------
| creator |
===========
-----------

What is your idea now?

Thanks,

Sandor

> <mailto:skosmos-users+unsub...@googlegroups.com>.

[Osma Suominen]

Hi Sandor!

Okay, so Skosmos is not seeing the triples you have in Fuseki. I'm
guessing this could be because of mismatches in named graphs. In a
SPARQL triple store there is always a default (unnamed) graph, and there
can also be multiple named graphs. If you have put e.g. the UNESCO
thesaurus in the default graph and configured Skosmos to use a named
graph, or vice versa, then that could explain why you don't see any content.

I suggest you put the UNESCO thesaurus in a named graph
<http://skos.um.es/unescothes/> (that's what we use as graph name). You
can upload it to Fuseki with the command line utility s-put that comes
with Fuseki, like this:

./s-put http://localhost:3030/ds/data http://skos.um.es/unescothes/
unescothes.ttl

(of course the Fuseki web interface can be used to do the same, just
make sure you upload to the correct named graph)

Then you should have the correct named graph in vocabularies.ttl
(skosmos:sparqlGraph setting) but you already seem to have that set
correctly.

-Osma

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[Sandor Kopacsi]

Dear Osma,

I have started Fuseki (with text index), downloaded unescothes.rdf to the local folder, and then executed the command:

./s-put http://localhost:3030/ds/data http://skos.um.es/unescothes/unescothes.ttl unescothes.rdf

Fuseki responded: 10:57:19 INFO  [26] PUT http://skosmos.phaidra.org:3030/ds/data?graph=http%3A%2F%2Fskos.um.es%2Funescothes%2Funescothes.ttl

so it seemed to be successful, but I still get the message from Skosmos:

 'The vocabulary does not contain terms beginning with "A"!' in the Alphabetical Tab of Skosmos' page, and in the Vocabulary information 

 panel all 'Term counts by language' are zero.

I also tried with the web interface of Fuseki, where from the Control Panel (after selecting "/ds") in the Graph field of the File upload section I have replaced default to http://skos.um.es/unescothes/unescothes.ttl but I got the same message in Skosmos.

What can be wrong?

Thanks,

Sandor

 

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[Osma Suominen]

Hi Sandor!

The s-put command line is wrong. The second argument should match the
graphName setting. Currently you have "unescothes.ttl" in there as well
so it's not the same graph. Please use the command line from my message.
Maybe there was a problem with line wrapping or copy/paste...

-Osma

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[Sandor Kopacsi]

Thank you, now it works! :-)

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[Sandor Kopacsi]

Dear Osma,

thank you again for your help with that I could make the UNESCO Thesaurus on the local Sparql Endpoint (Fuseki) work.

Since then I keep trying to use Skosmos for Getty TGN.

I have downloaded a sample record of Getty TGN (tgn_7011179.rdf - attached), and uploaded it to the ds dataset via the web interface of Fuseki selecting the default graph option. That was successful, 1021 triples have been loaded. The related section in vocabularies.ttl looks like this:

:tgnl a skosmos:Vocabulary, void:Dataset ;

        dc:title "TGN - Getty Thesaurus of Geographic Names - local"@en ;

        dc:subject :cat_general ;

        void:uriSpace "http://vocab.getty.edu/tgn";

        skosmos:language "en";

        skosmos:showTopConcepts "true";

        skosmos:loadExternalResources "false";

        skosmos:fullAlphabeticalIndex "true";

        skosmos:groupClass isothes:ConceptGroup ;

        skosmos:arrayClass isothes:ThesaurusArray ;

        void:sparqlEndpoint <http://localhost:3030/ds/sparql> ;

        skosmos:mainConceptScheme <http://vocab.getty.edu/tgn> .

When I select this vocabulary in Skosmos, sometimes (not always), I receive this message from the Fuseki server:

13:36:31 WARN  [6] Runtime IO Exception (client left?) RC = 500

13:36:31 INFO  [6] 500 org.eclipse.jetty.io.EofException (10.345 s)

and/or this:

11:32:40 INFO  [15] GET http://localhost:3030/ds/sparql?query=PREFIX+skos%3A+%3C                   http%3A%2F%2Fwww.w3.org%2F2004%2F02%2Fskos%2Fcore%23%3E%0ACONSTRUCT+%7B%0A++%3Ch                   ttp%3A%2F%2Fvocab.getty.edu%2Ftgn%3E+%3Fproperty+%3Fvalue+.%0A%7D+WHERE+%7B%0A++                   +%7B%0A++++%3Chttp%3A%2F%2Fvocab.getty.edu%2Ftgn%3E+%3Fproperty+%3Fvalue+.%0A+++                   +FILTER+%28%3Fproperty+%21%3D+skos%3AhasTopConcept%29%0A++%7D%0A%7D

11:32:40 INFO  [15] Query = PREFIX skos: <http://www.w3.org/2004/02/skos/core#>                    CONSTRUCT {   <http://vocab.getty.edu/tgn> ?property ?value . } WHERE {    {                        <http://vocab.getty.edu/tgn> ?property ?value .     FILTER (?property != skos:h                   asTopConcept)   } }

11:32:40 INFO  [15] exec/construct

11:32:40 INFO  [15] 200 OK (7 ms)

After that in the Alphabetical tab I can not see the content of TGN but the UNESCO vocabulary (shows Abadi->Awadhi, Adandoned children, etc.).  I have previously uploaded UNESCO vocabulary and used locally, but Fuseki server was stopped and restarted in the mean time. (I don't know how to stop Skosmos, I just closed the browser's page where I reached skosmos.) In case of TGN the Hierarchy tab is empty, but the Group index tab seems to contain Getty TGN (e.g. shows Countries and country groupings).

What can be the reason for that situation? 

Is there a cash of Fuseki or Skosmos that stores the previously used vocabularies?

Could it be the problem, that in a previous trial I have uploaded both the UNESCO and the TGN vocabulary to Fuseki to the same dataset (ds)? Is it possible to handle more than on vocabulary in the same dataset (ds) at the same time?

Why did I receive the Runtime IO Exception?

May be I don't really understand the concept of Skosmos and Fuseki, that is why I make such a mistakes. Can you suggest to read some documentations, that would make me understand better the usage of Skosmos and Fuseki?

Thank you very much,

Sandor

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[Osma Suominen]

Dear Sandor,

See replies below.

20.11.2015, 12:49, Sandor Kopacsi kirjoitti:
> thank you again for your help with that I could make the UNESCO
> Thesaurus on the local Sparql Endpoint (Fuseki) work.

Excellent!

> Since then I keep trying to use Skosmos for Getty TGN.
> I have downloaded a sample record of Getty TGN (tgn_7011179.rdf -
> attached), and uploaded it to the ds dataset via the web interface of
> Fuseki selecting the default graph option. That was successful, 1021
> triples have been loaded. The related section in vocabularies.ttl looks
> like this:
> :tgnl a skosmos:Vocabulary, void:Dataset ;
> dc:title "TGN - Getty Thesaurus of Geographic Names - local"@en ;
> dc:subject :cat_general ;
> void:uriSpace "http://vocab.getty.edu/tgn";
> skosmos:language "en";
> skosmos:showTopConcepts "true";
> skosmos:loadExternalResources "false";
> skosmos:fullAlphabeticalIndex "true";
> skosmos:groupClass isothes:ConceptGroup ;
> skosmos:arrayClass isothes:ThesaurusArray ;
> void:sparqlEndpoint <http://localhost:3030/ds/sparql> ;
> skosmos:mainConceptScheme <http://vocab.getty.edu/tgn> .

This configuration doesn't have a skosmos:sparqlGraph setting, which
implies that you are using the default graph, as you said.

The URI space is missing a slash, it should be:
void:uriSpace "http://vocab.getty.edu/tgn/";

I'm not sure about the mainConceptScheme setting, I think you better
remove it, it's probably not right and is not required.

> When I select this vocabulary in Skosmos, sometimes (not always), I
> receive this message from the Fuseki server:
> 13:36:31 WARN [6] Runtime IO Exception (client left?) RC = 500
> 13:36:31 INFO [6] 500 org.eclipse.jetty.io.EofException (10.345 s)

I think this is a timeout of some kind. Fuseki notices that the client
(i.e. Skosmos, unless you have Varnish or something as a proxy in the
middle?) gave up after about 10 seconds.

> and/or this:
>
> 11:32:40 INFO [15] GET
> http://localhost:3030/ds/sparql?query=PREFIX+skos%3A+%3C
>
> http%3A%2F%2Fwww.w3.org%2F2004%2F02%2Fskos%2Fcore%23%3E%0ACONSTRUCT+%7B%0A++%3Ch
>
> ttp%3A%2F%2Fvocab.getty.edu%2Ftgn%3E+%3Fproperty+%3Fvalue+.%0A%7D+WHERE+%7B%0A++
>
> +%7B%0A++++%3Chttp%3A%2F%2Fvocab.getty.edu%2Ftgn%3E+%3Fproperty+%3Fvalue+.%0A+++
>
> +FILTER+%28%3Fproperty+%21%3D+skos%3AhasTopConcept%29%0A++%7D%0A%7D
> 11:32:40 INFO [15] Query = PREFIX skos:
> <http://www.w3.org/2004/02/skos/core#> CONSTRUCT {
> <http://vocab.getty.edu/tgn> ?property ?value . } WHERE { {
> <http://vocab.getty.edu/tgn> ?property ?value . FILTER
> (?property != skos:h asTopConcept) } }
> 11:32:40 INFO [15] exec/construct
> 11:32:40 INFO [15] 200 OK (7 ms)

This is just a normal query by Skosmos. Not an error.

> After that in the Alphabetical tab I can not see the content of TGN but

> the UNESCO vocabulary (showsAbadi->Awadhi, Adandoned children, etc.). I

> have previously uploaded UNESCO vocabulary and used locally, but Fuseki
> server was stopped and restarted in the mean time. (I don't know how to
> stop Skosmos, I just closed the browser's page where I reached skosmos.)
> In case of TGN the Hierarchy tab is empty, but the Group index tab seems
> to contain Getty TGN (e.g. shows Countries and country groupings).

You are probably using the jena-text enabled configuration file with
Fuseki. That configuration file specifies directories where Fuseki
stores its data. If you have not modified the configuration, those will
be /tmp/tdb and /tmp/lucene. You need to clear/remove these directories
if you want to flush the Fuseki data.

> What can be the reason for that situation?
> Is there a cash of Fuseki or Skosmos that stores the previously used
> vocabularies?

Fuseki stores them in files. It is also possible to configure Fuseki for
in-memory only, but with a large dataset, that will require a lot of
memory. If you want to see how it is done, check out this Fuseki
configuration that we use for Skosmos unit tests:
https://github.com/NatLibFi/Skosmos/blob/master/tests/fuseki-assembler.ttl
(tdb:location and text:directory settings are the relevant ones)

> Could it be the problem, that in a previous trial I have uploaded both
> the UNESCO and the TGN vocabulary to Fuseki to the same dataset (ds)?

It seems that you uploaded both to the default graph, without
overwriting the old data.

> Is
> it possible to handle more than on vocabulary in the same dataset (ds)
> at the same time?

Yes, but then you need to use named graphs. There is only one default
graph (with no name), but there can be any number of named graphs on a
SPARQL endpoint/dataset. I suggest you use the URI namespaces as graph
names. I.e. <http://vocab.getty.edu/tgn/> would store TGN data.

> Why did I receive the Runtime IO Exception?

Not sure, maybe you have a short execution timeout for PHP scripts that
was triggered? See php.ini max_execution_time setting.

> May be I don't really understand the concept of Skosmos and Fuseki, that
> is why I make such a mistakes. Can you suggest to read some
> documentations, that would make me understand better the usage of
> Skosmos and Fuseki?

First of all, reading about SPARQL is recommended, especially dataset
management and named graphs. There are some good books such as "Learning
SPARQL", and of course the specifications are available though maybe not
the best introductory material.

The Fuseki documentation is highly recommended:
https://jena.apache.org/documentation/serving_data/

-Osma

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D.Sc. (Tech), Information Systems Specialist
National Library of Finland
P.O. Box 26 (Kaikukatu 4)
00014 HELSINGIN YLIOPISTO
Tel. +358 50 3199529
osma.s...@helsinki.fi

http://www.nationallibrary.fi

[Sandor Kopacsi]

Dear Osma,

thank you for your help again, that worked this time, too. 

Now I continue with Getty, because it would be very important for us to use either on-line or locally.

You wrote, that there can be problem with the on-line access of Getty because of the lack of  text index extension on the SPARQL Endpoints of Getty. That is way I think, that on my own SPARQL Endpoint with text index extension it might work.

I have downloaded the Getty AAT thesaurus (because it seems to be the smallest), and according to the instructions of Getty LOD (http://vocab.getty.edu/doc/#Total_Exports) I have uploaded to the Fuseki server (with text index) the skos.rdf, ontology.rdf and the first N-Triples file (AATOut_1Subjects.nt) using the Graph: http://vocab.getty.edu/aat/. All the three files have been uploaded successfully. In vocabularies.ttl I have set these parameters:

:aatl a skosmos:Vocabulary, void:Dataset ;

        dc:title "AATL - Getty Art & Architecture Thesaurus - local"@en ;

        dc:subject :cat_general ;

        void:uriSpace "http://vocab.getty.edu/aat/";

        skosmos:language "en";

        skosmos:showTopConcepts "true";

        skosmos:loadExternalResources "false";

        skosmos:fullAlphabeticalIndex "true";

      skosmos:groupClass isothes:ConceptGroup ;

        skosmos:arrayClass isothes:ThesaurusArray ;

        void:sparqlEndpoint <http://localhost:3030/ds/sparql> ;

        skosmos:sparqlGraph <http://vocab.getty.edu/aat/>.

From Skosmos I can see that there are 39 concepts, but neither form the Alphabetical, nor from the Hierarchy, and nor from the Group index there are no items visible. On the Alphabetical tag there is the usual message: "The vocabulary does not contain terms beginning with "A"!".

When I continue with the upload of the next N-Triples (AATOut_2Terms.nt - which is a rather huge file / ~ 400 MB) to Fuseki, I got the error message on Fuseki's page:

"Error 500: Java heap space

Fuseki - version 1.3.0 (Build date: 2015-07-25T17:11:28+0000)"

How can I fix this problem, and continue?

Thanks again,

Sandor

[Osma Suominen]

Dear Sandor,

You are making real progress!

The problem is related to loading data to Fuseki. This is not really a
Skosmos issue, but I can try to help.

The Fuseki file upload handling is not very good at processing large
files. It will load them first into memory, only then to the on-disk TDB
database (and also the Lucene/jena-text index in your case). It seems to
run out of memory on the first step ("OutOfMemoryError: java heap space"
is a typical error message when this happens).

You can try giving Fuseki more memory. See
https://github.com/NatLibFi/Skosmos/wiki/FusekiTuning for some tips. If
you give it several GB it should be able to handle a 400MB file upload
just fine, though it might take a while and you may want to restart
Fuseki afterwards to free some memory.

If that doesn't help, you will have to use offline loading of the data.
This means shutting down Fuseki (since only one process can use the TDB
at the same time) and using the tdbloader command line utilities to
create the TDB and load the RDF data. Then you will still need to
generate the text index as a separate step. A short tutorial of this is
included in the jena-text documentation:
https://jena.apache.org/documentation/query/text-query.html#building-a-text-index

Note that I haven't tried this myself.

You can also try asking for help on the Jena users mailing list, see
https://jena.apache.org/help_and_support/

-Osma

> "*Error 500: Java heap space*

> <http://localhost:3030/ds/sparql?query=PREFIX+skos%3A+%3C>
> >
> > http%3A%2F%2Fwww.w3.org
> <http://2Fwww.w3.org>%2F2004%2F02%2Fskos%2Fcore%23%3E%0ACONSTRUCT+%7B%0A++%3Ch
>
> >
> > ttp%3A%2F%2Fvocab.getty.edu
> <http://2Fvocab.getty.edu>%2Ftgn%3E+%3Fproperty+%3Fvalue+.%0A%7D+WHERE+%7B%0A++
>
> >
> > +%7B%0A++++%3Chttp%3A%2F%2Fvocab.getty.edu
> <http://2Fvocab.getty.edu>%2Ftgn%3E+%3Fproperty+%3Fvalue+.%0A+++

> osma.s...@helsinki.fi <javascript:>
> http://www.nationallibrary.fi
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[Sandor Kopacsi]

Dear Osma,

Thank you again for your help.

In the mean time I got more memory on the virtual machine, and I have extended the available memory for the Java VM up to 8 GB (JVM_ARGS=-Xmx8000M).

I have uploaded to the Fuseki server (with text index) the skos.rdf, ontology.rdf and all the N-Triples files of Getty AAT thesaurus successfully using the http://vocab.getty.edu/aat/ Graph for upload.

In vocabularies.ttl I still use these parameters:

:aatl a skosmos:Vocabulary, void:Dataset ;

        dc:title "AATL - Getty Art & Architecture Thesaurus - local"@en ;

        dc:subject :cat_general ;

        void:uriSpace "http://vocab.getty.edu/aat/";

        skosmos:language "en";

        skosmos:showTopConcepts "true";

        skosmos:loadExternalResources "false";

        skosmos:fullAlphabeticalIndex "true";

      skosmos:groupClass isothes:ConceptGroup ;

        skosmos:arrayClass isothes:ThesaurusArray ;

        void:sparqlEndpoint <http://localhost:3030/ds/sparql> ;

        skosmos:sparqlGraph <http://vocab.getty.edu/aat/>.

After that trying to open the Getty AAT from Skosmos I still experience, that I can see in the Vocabulary information sheet that 39 concepts have been uploaded, but they are not visible either form the Alphabetical, or from the Hierarchy, or from the Group index tabs. On the Alphabetical tab there is the a message says: "The vocabulary does not contain terms beginning with "A"!".

What could be the next step to make Getty AAT visible in Skosmos.

Thank you very much!

Sandor

> <mailto:skosmos-users+unsub...@googlegroups.com>.

[Osma Suominen]

Hi Sandor!

Your configuration seems OK. I wouldn't recommend using
fullAlphabeticalIndex for such a large vocabulary, but that's not the
reason for your problems.

I wonder whether your data is OK. You say you've loaded everything into
the graph, but have you checked what's actually in there? For example
these SPARQL queries that you could execute in the Fuseki user interface
could help to see if there are any problems:

1. The amount of triples in the graph

SELECT (COUNT(*) AS ?count) {
GRAPH <http://vocab.getty.edu/aat/> { ?s ?p ?o }
}

This should be a large number, maybe 10 or 20 times the number of concepts.

2. The number of SKOS concepts

PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT (COUNT(*) AS ?count) {
GRAPH <http://vocab.getty.edu/aat/> {
?s a skos:Concept
}
}

3. The number of SKOS prefLabels

PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT (COUNT(*) AS ?count) {
GRAPH <http://vocab.getty.edu/aat/> {
?s skos:prefLabel ?label
}
}

Is it possible that while loading the data from several files, you have
overwritten the previous data when loading a new file? That's what s-put
does - it clears the graph first. You should use s-post if you want to
add to existing data without clearing it.

-Osma

On 16/12/15 17:07, Sandor Kopacsi wrote:
> Dear Osma,
>

> <http://vocab.getty.edu/doc/#Total_Exports>) I have uploaded to the

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>
>
> --
> Osma Suominen
> D.Sc. (Tech), Information Systems Specialist
> National Library of Finland
> P.O. Box 26 (Kaikukatu 4)
> 00014 HELSINGIN YLIOPISTO
> Tel. +358 50 3199529
> osma.s...@helsinki.fi <javascript:>
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[Sandor Kopacsi]

Dear Osma,

Thank you for your help again.

After starting the Fuseki server with text index (./fuseki-server --config jena-text-config.ttl where jena-text-config.ttl is attached) I used the suggested s-post as follow

./s-post http://localhost:3030/ds/data http://vocab.getty.edu/aat/{required rdf or nt files} 

instead of manual upload from the Control panel of Fuseki or using s-put that I both did so far. (By the way, do you know, that the manual upload uses s-put or s-post?)

I checked after each s-post statement the amount of triples in the graph, that increased nice continuously up to 12151134. By the end of the uploading of the 19 files (skos.rdf, ontology.rdf as well as 17 Getty AAT files) the number of SKOS concepts were still 39 only, and the number of SKOS prefLabels reached 2283.

Unfortunately the result on Skosmos is still the same: I can see in the Vocabulary information sheet that 39 concepts have been uploaded, but they are not visible either form the Alphabetical, or from the Hierarchy, or from the Group index tabs. On the Alphabetical  tab there is the a message says: "The vocabulary does not contain terms beginning with "A"!". 

Do you have any other idea, what should I modify next?

Thank you very much again!

Best regards,

Sandor

 

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>     --
>     Osma Suominen
>     D.Sc. (Tech), Information Systems Specialist
>     National Library of Finland
>     P.O. Box 26 (Kaikukatu 4)
>     00014 HELSINGIN YLIOPISTO
>     Tel. +358 50 3199529
>     osma.s...@helsinki.fi <javascript:>
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[Sandor Kopacsi]

Dear Osma,

Thank you for your help again.

After starting the Fuseki server with text index (./fuseki-server --config jena-text-config.ttl where jena-text-config.ttl is attached) I used the suggested s-post as follow

./s-post http://localhost:3030/ds/data http://vocab.getty.edu/aat/{required rdf or nt files} 

instead of manual upload from the Control panel of Fuseki or using s-put that I both did so far. (By the way, do you know, that the manual upload uses s-put or s-post?)

I checked after each s-post statement the amount of triples in the graph, that increased nice continuously up to 12151134. By the end of the uploading of the 19 files (skos.rdf, ontology.rdf as well as 17 Getty AAT files) the number of SKOS concepts were still 39 only, and the number of SKOS prefLabels reached 2283.

Unfortunately the result on Skosmos is still the same: I can see in the Vocabulary information sheet that 39 concepts have been uploaded, but they are not visible either form the Alphabetical, or from the Hierarchy, or from the Group index tabs. On the Alphabetical  tab there is the a message says: "The vocabulary does not contain terms beginning with "A"!". 

Do you have any other idea, what should I modify next?

Thank you very much again!

Best regards,

Sandor

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>
>     --
>     Osma Suominen
>     D.Sc. (Tech), Information Systems Specialist
>     National Library of Finland
>     P.O. Box 26 (Kaikukatu 4)
>     00014 HELSINGIN YLIOPISTO
>     Tel. +358 50 3199529
>     osma.s...@helsinki.fi <javascript:>
>     http://www.nationallibrary.fi
>
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[Osma Suominen]

Dear Sandor,

Okay so the number of triples (12M) sounds about right. But the number
of concepts and prefLabels seem to be too low.

I wonder if this is due to (lack of) inference. Which set of AAT files
[1] did you use? They have the "explicit" set and the "full" set (aka
Total Exports). With the "explicit" set, which is smaller, you will need
to configure Fuseki to use inference so that the data store can infer
the missing triples. With the full set this is not needed, but in turn
the data set is much larger so you may have difficulties loading it (I
wouldn't try loading that through Fuseki, but it could work with
tdbloader as I explained in a previous message).

As for configuring inference in Fuseki, I'm afraid I can't help much
since I've never done it. You will have to do some research (a search
for "fuseki inference" at least gets you some hits). There is some
documentation [2] about configuring inference in Jena assembler files
(such as the Fuseki configuration file). If that doesn't help, you can
asks on the Jena users' mailing list or on forums such as StackOverflow.

-Osma


[1] http://vocab.getty.edu/doc/#Export_Files
[2] https://jena.apache.org/documentation/assembler/assembler-howto.html

On 18/12/15 14:54, Sandor Kopacsi wrote:
> Dear Osma,
>

> Thank you for your help again.
>
> After starting the Fuseki server with text index (./fuseki-server
> --config jena-text-config.ttl where jena-text-config.ttl is attached) I
> used the suggested s-post as follow
>

> *./s-post http://localhost:3030/ds/data
> http://vocab.getty.edu/aat/{required rdf or nt files}*

>
> instead of manual upload from the Control panel of Fuseki or using s-put
> that I both did so far. (By the way, do you know, that the manual upload
> uses s-put or s-post?)
>
> I checked after each s-post statement the amount of triples in the
> graph, that increased nice continuously up to 12151134. By the end of
> the uploading of the 19 files (skos.rdf, ontology.rdf as well as 17

> Getty AAT files) the *number of SKOS concepts were still 39 only*,

> > > <mailto:skosmos-user...@googlegroups.com
> <javascript:> <javascript:>>.

> > an email to skosmos-user...@googlegroups.com <javascript:>
> > <mailto:skosmos-user...@googlegroups.com <javascript:>>.

> > To post to this group, send email to skosmo...@googlegroups.com
> <javascript:>
> > <mailto:skosmo...@googlegroups.com <javascript:>>.
> > To view this discussion on the web visit
> >

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>

> > For more options, visit https://groups.google.com/d/optout
> <https://groups.google.com/d/optout>.
>
>
> --
> Osma Suominen
> D.Sc. (Tech), Information Systems Specialist
> National Library of Finland
> P.O. Box 26 (Kaikukatu 4)
> 00014 HELSINGIN YLIOPISTO
> Tel. +358 50 3199529
> osma.s...@helsinki.fi <javascript:>
> http://www.nationallibrary.fi
>
> --
> You received this message because you are subscribed to the Google
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[Sandor Kopacsi]

Dear Osma, 

I have used the "explicit" set, so it means, that with it I should configure Fuseki to use inference...

I will check the suggested sources, thank you. 

If I understand well, if the configuration for inference doesn't help, I can download the "full" set, and use tdbloader.
The problem is that I don't have any tdbloader. 

Should have come it with Fuseki, or is part of Jena, that I should have download separately?

 

I understand, that these fields are out of your scope, and I will ask on Jena users' mailing list. 

If I will have problems with Skosmos again. I will come back to you :-)

Thank you very much for all your help, and I wish you Merry Christmas and Happy New Year!

Best Regards,

Sandor

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>
>     --
>     Osma Suominen
>     D.Sc. (Tech), Information Systems Specialist
>     National Library of Finland
>     P.O. Box 26 (Kaikukatu 4)
>     00014 HELSINGIN YLIOPISTO
>     Tel. +358 50 3199529
>     osma.s...@helsinki.fi <javascript:>
>     http://www.nationallibrary.fi
>
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[Osma Suominen]

Dear Sandor,

You are correct, your options are either to 1) set up inferencing or 2)
use the "full" dataset with tdbloader.

tdbloader is part of the Jena distribution which you will need to
download separately. A tutorial for using tdbloader with the text index
is here:
https://jena.apache.org/documentation/query/text-query.html#building-a-text-index

Merry Christmas to you too!

-Osma

On 21/12/15 10:46, Sandor Kopacsi wrote:
> Dear Osma,
>

> <http://www.google.com/url?q=http%3A%2F%2Fvocab.getty.edu%2Fdoc%2F%23Export_Files&sa=D&sntz=1&usg=AFQjCNGs7dIUfW2_gHL9nXiMZVybWpCGwA>
>
> [2]
> https://jena.apache.org/documentation/assembler/assembler-howto.html
> <https://www.google.com/url?q=https%3A%2F%2Fjena.apache.org%2Fdocumentation%2Fassembler%2Fassembler-howto.html&sa=D&sntz=1&usg=AFQjCNFM1whzFFv1NGeIhFxOfS0tgaw3zA>

>
>
> On 18/12/15 14:54, Sandor Kopacsi wrote:
> > Dear Osma,
> >
> > Thank you for your help again.
> >
> > After starting the Fuseki server with text index (./fuseki-server
> > --config jena-text-config.ttl where jena-text-config.ttl is
> attached) I
> > used the suggested s-post as follow
> >
> > *./s-post http://localhost:3030/ds/data
> > http://vocab.getty.edu/aat/{required

> <http://vocab.getty.edu/aat/%7Brequired> rdf or nt files}*

> > > > <mailto:skosmos-user...@googlegroups.com
> <javascript:>

> > > <mailto:skosmos-user...@googlegroups.com

> <javascript:> <javascript:>>.
> > > To post to this group, send email to
> skosmo...@googlegroups.com
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> > > <mailto:skosmo...@googlegroups.com <javascript:>>.
> > > To view this discussion on the web visit
> > >
> >

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>
> >
> > >
> >
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>
> >
> > > For more options, visit https://groups.google.com/d/optout
> <https://groups.google.com/d/optout>

> > <https://groups.google.com/d/optout
> <https://groups.google.com/d/optout>>.
> >
> >
> > --
> > Osma Suominen
> > D.Sc. (Tech), Information Systems Specialist
> > National Library of Finland
> > P.O. Box 26 (Kaikukatu 4)
> > 00014 HELSINGIN YLIOPISTO
> > Tel. +358 50 3199529
> > osma.s...@helsinki.fi <javascript:>
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>

> > For more options, visit https://groups.google.com/d/optout
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>
> --
> Osma Suominen
> D.Sc. (Tech), Information Systems Specialist
> National Library of Finland
> P.O. Box 26 (Kaikukatu 4)
> 00014 HELSINGIN YLIOPISTO
> Tel. +358 50 3199529
> osma.s...@helsinki.fi <javascript:>
> http://www.nationallibrary.fi
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[Sandor Kopacsi]

Dear Osma,

Happy New Year and thank you for your help on jena mailing list, too. :-)

Now I write here again because I overcame the problem of fuseki's tbdloader (at least it seems so to me), and now unfortunately I have problems again with skosmos for using getty's vocabulary.

I have used the tbd loader of fuseki  for the full dataset of aat as follow:

java -cp /fuseki-server.jar tdb.tdbloader --tdb=jena-text-config.ttl --graph=http://vocab.getty.edu/aat/  ./vocabularies/getty_aat/full/ontology.rdf

java -cp /fuseki-server.jar tdb.tdbloader --tdb=jena-text-config.ttl --graph=http://vocab.getty.edu/aat/  ./vocabularies/getty_aat/full/skos.rdf

java -cp /fuseki-server.jar tdb.tdbloader --tdb=jena-text-config.ttl --graph=http://vocab.getty.edu/aat/  ./vocabularies/getty_aat/full/AATOut_Full.nt

java -cp /fuseki-server.jar tdb.tdbloader --tdb=jena-text-config.ttl --graph=http://vocab.getty.edu/aat/  ./vocabularies/getty_aat/full/AATOut_Contribs.nt

java -cp /fuseki-server.jar tdb.tdbloader --tdb=jena-text-config.ttl --graph=http://vocab.getty.edu/aat/  ./vocabularies/getty_aat/full/AATOut_Sources.nt

After that I built the text index with 

java -cp ./fuseki-server.jar jena.textindexer --desc=jena-text-config.ttl

(I am not sure if I should use here the --graph option.)

Then I have started fuseki and run the query

SELECT (COUNT(*) AS ?count) { 

   GRAPH <http://vocab.getty.edu/aat/> { ?s ?p ?o } 

} 

from fuseki's control panel, which counted the amount of triples as 17.037.361, that looked promising.

Finaly I started skosmos, and selected Getty AAT described in vocabularies.ttl as follow:

:aatl a skosmos:Vocabulary, void:Dataset ;

        dc:title "AATL - Getty Art & Architecture Thesaurus - local"@en ;

        dc:subject :cat_general ;

        void:uriSpace "http://vocab.getty.edu/aat/";

        skosmos:language "en";

        skosmos:showTopConcepts "true";

        skosmos:loadExternalResources "false";

        skosmos:fullAlphabeticalIndex "true";

      skosmos:groupClass isothes:ConceptGroup ;

        skosmos:arrayClass isothes:ThesaurusArray ;

        void:sparqlEndpoint <http://localhost:3030/ds/sparql> ;

        skosmos:sparqlGraph <http://vocab.getty.edu/aat/>.

Skosmos shows on the Vocabulary information sheet that number of concepts are 40.815, but then it keeps loading endless.

On the console of fuseki it writes:

...

18:13:41 WARN  [9] Runtime IO Exception (client left?) RC = 500

18:13:41 INFO  [9] 500 org.eclipse.jetty.io.EofException (61.656 s)

and nothing happens.

What can be the problem now?

Thank you for your help again!

Best Regards,

Sandor

>      >      >      > <mailto:skosmos-users+unsub...@googlegroups.com

[Osma Suominen]

Dear Sandor,

Happy New Year to you too!

I'm also on the Jena mailing lists since I use Jena a lot and help
maintain the jena-text module, but I sent you there because there are a
lot of very knowledgeable people like Andy who know the Jena suite much
better than I do.

It seems you've succeeded loading the data properly. The problem sounds
like a timeout to me. There is simply a lot of data in AAT, more than
Skosmos is made to handle, so some queries can take a very long time.
Based on the error message I think you have a 60 second timeout
somewhere, either in Apache (TimeOut directive), PHP (max_execution_time
setting) or Varnish (first_byte_timeout and between_bytes_timeout). I
suggest finding the setting and changing it to a higher value (say 5 or
10 minutes).

The slow queries are probably the statistical queries (number of
concepts per type, number of labels per language) as well as the
alphabetical index. For the statistical queries, we are making them
optional in Skosmos 1.5 but this is not yet implemented, see
https://github.com/NatLibFi/Skosmos/issues/413

I hope you've set up Varnish in between Skosmos/Apache and Fuseki? You
definitely should. It doesn't help with the first request, but
subsequent ones will be answered very quickly from the cache. The
statistical queries are always the same so they can be cached very well.
See https://github.com/NatLibFi/Skosmos/wiki/FusekiTuning#http-caching

Hope this helps!

-Osma

On 13/01/16 19:39, Sandor Kopacsi wrote:
> Dear Osma,
>

> <http://vocab.getty.edu/doc/#Export_Files>
> >
> <http://www.google.com/url?q=http%3A%2F%2Fvocab.getty.edu%2Fdoc%2F%23Export_Files&sa=D&sntz=1&usg=AFQjCNGs7dIUfW2_gHL9nXiMZVybWpCGwA

> <http://www.google.com/url?q=http%3A%2F%2Fvocab.getty.edu%2Fdoc%2F%23Export_Files&sa=D&sntz=1&usg=AFQjCNGs7dIUfW2_gHL9nXiMZVybWpCGwA>>
>
> >
> > [2]
> >
> https://jena.apache.org/documentation/assembler/assembler-howto.html

> <https://jena.apache.org/documentation/assembler/assembler-howto.html>
> >
> <https://www.google.com/url?q=https%3A%2F%2Fjena.apache.org%2Fdocumentation%2Fassembler%2Fassembler-howto.html&sa=D&sntz=1&usg=AFQjCNFM1whzFFv1NGeIhFxOfS0tgaw3zA

> <https://www.google.com/url?q=https%3A%2F%2Fjena.apache.org%2Fdocumentation%2Fassembler%2Fassembler-howto.html&sa=D&sntz=1&usg=AFQjCNFM1whzFFv1NGeIhFxOfS0tgaw3zA>>
>
> >
> >
> > On 18/12/15 14:54, Sandor Kopacsi wrote:
> > > Dear Osma,
> > >
> > > Thank you for your help again.
> > >
> > > After starting the Fuseki server with text index
> (./fuseki-server
> > > --config jena-text-config.ttl where jena-text-config.ttl is
> > attached) I
> > > used the suggested s-post as follow
> > >
> > > *./s-post http://localhost:3030/ds/data
> > > http://vocab.getty.edu/aat/{required
> <http://vocab.getty.edu/aat/%7Brequired>

> > <http://vocab.getty.edu/aat/%7Brequired

> <mailto:skosmos-user...@googlegroups.com <javascript:>

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--
Osma Suominen
D.Sc. (Tech), Information Systems Specialist
National Library of Finland
P.O. Box 26 (Kaikukatu 4)
00014 HELSINGIN YLIOPISTO
Tel. +358 50 3199529
osma.s...@helsinki.fi

http://www.nationallibrary.fi

[Sandor Kopacsi]

Dear Osma,

Thank you again!

I have changed both the Apache's Timeout and PHP's max_execution_time to 600, but the Runtime IO Exception comes again (and much earlier than 600 seconds):

11:33:07 INFO  [10] exec/select

11:33:07 INFO  [10] 200 OK (16.649 s)

11:33:39 INFO  [11] exec/select

11:33:41 WARN  [11] Runtime IO Exception (client left?) RC = 500

11:33:41 INFO  [11] 500 org.eclipse.jetty.io.EofException (50.009 s)

Varnish is not yet installed, but you wrote, that it would not help with the first request.

The problem can be something else, or I should install and set Varnish now?

Best Regards,

Sandor

[Osma Suominen]

Dear Sandor,

Okay, maybe it's the browser timing out. You could also check the Apache
error.log in case there are warnings or errors there that could indicate
why the SPARQL query is terminated. This time it happened at almost
exactly 50 seconds, which also looks like some kind of a timeout.

In any case, you don't actually need to wait for the missing items to
load, you could still use other functionalities of Skosmos. You can try
browsing the alphabetical index, or doing searches. Does that work for you?

-Osma

On 14/01/16 12:49, Sandor Kopacsi wrote:
> Dear Osma,

> > --graph=http://vocab.getty.edu/aat/ <http://vocab.getty.edu/aat/>

> > ./vocabularies/getty_aat/full/ontology.rdf
> > java -cp /fuseki-server.jar tdb.tdbloader --tdb=jena-text-config.ttl

> > --graph=http://vocab.getty.edu/aat/ <http://vocab.getty.edu/aat/>

> ./vocabularies/getty_aat/full/skos.rdf
> > java -cp /fuseki-server.jar tdb.tdbloader --tdb=jena-text-config.ttl

> > --graph=http://vocab.getty.edu/aat/ <http://vocab.getty.edu/aat/>

> > ./vocabularies/getty_aat/full/AATOut_Full.nt
> > java -cp /fuseki-server.jar tdb.tdbloader --tdb=jena-text-config.ttl

> > --graph=http://vocab.getty.edu/aat/ <http://vocab.getty.edu/aat/>

> > ./vocabularies/getty_aat/full/AATOut_Contribs.nt
> > java -cp /fuseki-server.jar tdb.tdbloader --tdb=jena-text-config.ttl

> > --graph=http://vocab.getty.edu/aat/ <http://vocab.getty.edu/aat/>

> > > > <http://2Fvocab.getty.edu>

> > >
>
> --
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[Sandor Kopacsi]

Dear Osma,

you are right, it is partly browser dependent. I set the Timeout of IE (KeepAliveTimeout) to 10 minutes, and disabled the Timeout of Firefox (enabletimeout set to false), in Chrome it is not possible. In IE and Firefox I could go a bit further: they show the number of terms (41843 as preferred terms and 105126 as alternate terms), which can not be calculated in Chrome, but after a few seconds I got the same Runtime IO Exception:

18:20:41 INFO  [47] 200 OK (15.632 s)

18:21:06 INFO  [50] exec/select

18:21:06 WARN  [50] Runtime IO Exception (client left?) RC = 500

18:21:06 INFO  [50] 500 org.eclipse.jetty.io.EofException (40.422 s)

In the error-skosmos.log file I found:

[Thu Jan 14 18:20:36 2016] [error] [client 131.130.2.250] PHP Fatal error:  Uncaught exception 'EasyRdf_Exception' with message 'Request to localhost:3030 timed out' in /var/www/skosmos/vendor/easyrdf/easyrdf/lib/EasyRdf/Http/Client.php:458\nStack trace:\n#0 /var/www/skosmos/vendor/easyrdf/easyrdf/lib/EasyRdf/Sparql/Client.php(276): EasyRdf_Http_Client->request()\n#1 /var/www/skosmos/vendor/easyrdf/easyrdf/lib/EasyRdf/Sparql/Client.php(120): EasyRdf_Sparql_Client->request('query', 'SELECT DISTINCT...')\n#2 /var/www/skosmos/model/sparql/GenericSparql.php(754): EasyRdf_Sparql_Client->query('SELECT DISTINCT...')\n#3 /var/www/skosmos/model/Vocabulary.php(706): GenericSparql->queryConceptsAlphabetical('*', 'en', NULL, NULL, Array)\n#4 /var/www/skosmos/controller/WebController.php(477): Vocabulary->searchConceptsAlphabetical('*', NULL, NULL, 'en')\n#5 /var/www/skosmos/index.php(85): WebController->invokeAlphabeticalIndex(Object(Request))\n#6 {main}\n  thrown in /var/www/skosmos/vendor/easyrdf/easyrdf/lib/EasyRdf/Http/Client.php on line 458, referer: http://skosmos.phaidra.org/aatl/en/

which seems to be a timeout error, but I don't know where else I can modify the time out setting.

If I try in Skosmos the Alphabetical, the Hierarchy or the Group index view, the situation is the same: keep trying, and after a few seconds (not minutes) comes the Runtime IO Exception. If I search for a single letter it says: 

No vocabularies on the server!

Thanks again,

Sandor

English

41843

105126

0

[Osma Suominen]

Dear Sandor,

Operations timing out are no surprise, though I'm not sure where the
timeout values come from.

I forgot last time that Skosmos has a HTTP_TIMEOUT setting in
config.inc, you could see if increasing that to a large value helps. It
should only be used for external URI requests, not for regular SPARQL
queries, but there may be unknown side-effects.

Also the EasyRdf HTTP client has a default timeout of 10 seconds. You
could see if editing it helps. It is set in
vendor/easyrdf/easyrdf/lib/EasyRdf/Http/Client.php near the top of the
class definition.
(If you change this then an update of EasyRdf might revert your changes
later on, but at least we know where the timeout is being set)


The search for single letter error "No vocabularies on the server!" is
strange. Do you get it directly or only after a delay? Have you
configured jena-text properly? Please check the following:

1. You have this line in config.inc:
define("DEFAULT_SPARQL_DIALECT", "JenaText");

2. You are using a Fuseki assembler configuration with jena-text, i.e.
the one from here:
https://github.com/NatLibFi/Skosmos/wiki/InstallFusekiJenaText

3. You have built the jena-text index using jena.textindexer:
http://jena.staging.apache.org/documentation/query/text-query.html#step-2-build-the-text-index

Please also try searching for a whole word that you know exists in AAT,
for example "architecture", not just a single letter.

Hope this helps!

-Osma

> <http://vocab.getty.edu/aat/> <http://vocab.getty.edu/aat/>

> > > ./vocabularies/getty_aat/full/ontology.rdf
> > > java -cp /fuseki-server.jar tdb.tdbloader
> --tdb=jena-text-config.ttl
> > > --graph=http://vocab.getty.edu/aat/

> <http://vocab.getty.edu/aat/> <http://vocab.getty.edu/aat/>

> > ./vocabularies/getty_aat/full/skos.rdf
> > > java -cp /fuseki-server.jar tdb.tdbloader
> --tdb=jena-text-config.ttl
> > > --graph=http://vocab.getty.edu/aat/

> <http://vocab.getty.edu/aat/> <http://vocab.getty.edu/aat/>

> > > ./vocabularies/getty_aat/full/AATOut_Full.nt
> > > java -cp /fuseki-server.jar tdb.tdbloader
> --tdb=jena-text-config.ttl
> > > --graph=http://vocab.getty.edu/aat/

> <http://vocab.getty.edu/aat/> <http://vocab.getty.edu/aat/>

> > > ./vocabularies/getty_aat/full/AATOut_Contribs.nt
> > > java -cp /fuseki-server.jar tdb.tdbloader
> --tdb=jena-text-config.ttl
> > > --graph=http://vocab.getty.edu/aat/

> <http://vocab.getty.edu/aat/> <http://vocab.getty.edu/aat/>

> --
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[Sandor Kopacsi]

Dear Osma,

thank you again for your helpful suggestions.

Changing the HTTP_TIMEOUT setting in config.inc and the timeout setting in vendor/easyrdf/easyrdf/lib/EasyRdf/Http/Client.php finally eliminated the time out errors.

Now Skosmos works locally with Getty TGN fairly well. Sometimes it is rather slow, but acceptable. It shows better performance in IE than in Firefox or in Crome (where I could not change the browser's timeout, but it was not the problem.)

Now I am browsing the Getty TGN data set, and one feature of Skosmos is not really clear to me. It can show the Hierarchy only after searching an item in the search field, or selecting concept in the content pane. Without that the "Hierarchy" Tab is empty. Is there any option with which I can show the Hierarchy (strating from its root) by default of the entire data set?

My other question is, why are the content of the "Group index" and the "Alphabetical" tabs always empty? ("Alphabetical" says "Loading more items", but nothing happens.) Is there any setting with which I can show the "Group index" and / or the "Alphabetical" content? By the way, what should they actually show?

If it is not possible, is there any option with which I can delete the entire "Group index" and / or the "Alphabetical" tabs somehow to leave the only working "Hierarchy" tab there alone?

Thanks again,

Sandor

[Osma Suominen]

Dear Sandor,

I'm glad to hear that you finally got AAT working in Skosmos!

As to your issues:

1. Hierarchy. Try setting "skosmos:showTopConcepts true" in your
vocabularies.ttl file. That should display the top level hierarchy -
assuming that the AAT data contains the skos:hasTopConcept and/or
skos:topConceptOf relationships that are necessary for this to work.

2. Group index. This is meant for thematic groups, often represented as
skos:Collection or iso-thes:ConceptGroup. I'm not sure whether the AAT
has these at all and in that case how they are represented in RDF. If
you don't need this tab, simply drop the skosmos:groupClass setting from
vocabularies.ttl.

3. Alphabetical index. Do you still have the
skosmos:fullAlphabeticalIndex setting enabled in vocabularies.ttl, as in
the file you posted some time ago? It is meant for small vocabularies
(maybe 100-200 concepts maximum) and is totally unsuitable for such a
large vocabulary. Try removing that setting if it helps. Other than
that, the alphabetical index might just be very slow to load for such a
large vocabulary - see if you can adjust the timeouts further.
Unfortunately it is a core feature and cannot be disabled completely in
Skosmos currently.

I assume you have the text index working properly since you mentioned
searching. The alphabetical index also relies heavily on the text index
and will not work without a text index except for very small
vocabularies. See my previous message about setting up the text index.

If you want to see these tabs in action, check out the Skosmos demo site
http://skosmos.dev.finto.fi or Finto at http://finto.fi

-Osma

[Sandor Kopacsi]

Dear Osma,

Thanks to your help now Getty's TGN, AAT as well as ULAN works well with Skosmos using our local SPARQL server.

I tried again with the remote SPARQL server of Getty, using the following settings in vocabularies.ttl, but it still doesn't work.  

:aato a skosmos:Vocabulary, void:Dataset ;

        dc:title "Getty AAT - Art & Architecture Thesaurus - online"@en ;

        dc:subject :cat_general ;

        void:uriSpace "http://vocab.getty.edu/aat/";

        skosmos:language "en";

        skosmos:showTopConcepts "true";

        skosmos:loadExternalResources "true";

        skosmos:fullAlphabeticalIndex "true";

        skosmos:arrayClass isothes:ThesaurusArray ;

        void:sparqlEndpoint <http://vocab.getty.edu/sparql/> ;

        skosmos:sparqlGraph <http://vocab.getty.edu/aat>.

And I got this server error:

[Wed Feb 10 17:31:37 2016] [error] [client 131.130.2.250] PHP Fatal error:  Call to a member function getValue() on a non-object in /var/www/skosmos/model/Vocabulary.php on line 146, referer: http://skosmos.phaidra.org/en/?clang=

Can the problem still relay on that the SPARQL server of Getty doesn't use text index?

I have started to deal with another classification schema, i.e. ÖFOS 2012 - Österreichische Systematik der Wissenschaftszweige. I could download the classifications in csv format, converted to xml then to rdf format.

Using the control panel of Jena-Fuseki I uploaded the rdf files (one contains the structure, the other the alphabet - see attached) of ÖFOS to the default graph.

How can I display them in Skosmos without knowing its uriSpace? I used the following settings:

:oefoso a skosmos:Vocabulary, void:Dataset ;

        dc:title "ÖFOS 2012 - Österreichische Systematik der Wissenschaftszweige - local !"@en ;

         dc:subject :cat_general ;

         skosmos:language "en";

         skosmos:showTopConcepts "true";

         skosmos:loadExternalResources "false";

         skosmos:fullAlphabeticalIndex "true";

         skosmos:arrayClass isothes:ThesaurusArray ;

         void:sparqlEndpoint <http://localhost:3030/ds/sparql> ;

         .

Thanks in advance again!

Best Regards,

Sandor

[Osma Suominen]

Dear Sandor,

Please find my comments below.

10.02.2016, 18:51, Sandor Kopacsi kirjoitti:
> Dear Osma,

> Thanks to your help now Getty's TGN, AAT as well as ULAN works well with
> Skosmos using our local SPARQL server.
> I tried again with the remote SPARQL server of Getty, using the
> following settings in vocabularies.ttl, but it still doesn't work.
> :aato a skosmos:Vocabulary, void:Dataset ;
> dc:title "Getty AAT - Art & Architecture Thesaurus - online"@en ;
> dc:subject :cat_general ;
> void:uriSpace "http://vocab.getty.edu/aat/";
> skosmos:language "en";
> skosmos:showTopConcepts "true";
> skosmos:loadExternalResources "true";
> skosmos:fullAlphabeticalIndex "true";
> skosmos:arrayClass isothes:ThesaurusArray ;
> void:sparqlEndpoint <http://vocab.getty.edu/sparql/> ;
> skosmos:sparqlGraph <http://vocab.getty.edu/aat>.
>
> And I got this server error:
>
> [Wed Feb 10 17:31:37 2016] [error] [client 131.130.2.250] PHP Fatal
> error: Call to a member function getValue() on a non-object in
> /var/www/skosmos/model/Vocabulary.php on line 146, referer:
> http://skosmos.phaidra.org/en/?clang=
>
> Can the problem still relay on that the SPARQL server of Getty doesn't
> use text index?

The error you are seeing is probably not caused by the lack of a text
index. I'm not sure which version of Skosmos you are using, since
neither the original 1.4 release, the current 1.4-maintenance branch,
nor the current master branch have a getValue() call on line 146 in
model/Vocabulary.php, but this seems related to retrieving information
about the concept scheme.

However, even if this particular problem were fixed, the lack of a text
index would most likely prevent any actual use of Skosmos with the Getty
endpoint. Skosmos simply needs to have a text index to work with
vocabularies of medium to large size. The limit is perhaps a few
thousand concepts, depending on the performance of the endpoint / triple
store and how much delay users are willing to accept, but Getty
vocabularies have many more than that.

> I have started to deal with another classification schema, i.e. ÖFOS
> 2012 - Österreichische Systematik der Wissenschaftszweige. I could
> download the classifications in csv format, converted to xml then to rdf
> format.
> Using the control panel of Jena-Fuseki I uploaded the rdf files (one
> contains the structure, the other the alphabet - see attached) of ÖFOS
> to the default graph.
> How can I display them in Skosmos without knowing its uriSpace? I used
> the following settings:
>
> :oefoso a skosmos:Vocabulary, void:Dataset ;
> dc:title "ÖFOS 2012 - Österreichische Systematik der
> Wissenschaftszweige - local !"@en ;
> dc:subject :cat_general ;
> skosmos:language "en";
> skosmos:showTopConcepts "true";
> skosmos:loadExternalResources "false";
> skosmos:fullAlphabeticalIndex "true";
> skosmos:arrayClass isothes:ThesaurusArray ;
> void:sparqlEndpoint <http://localhost:3030/ds/sparql> ;

The files you sent do not look like SKOS at all. The structure file is
CSV, not RDF at all, maybe you sent the wrong file? The alphabetical
file is RDF, but not SKOS. It looks like the result of some CSV to RDF
conversion tool. Skosmos cannot work with data like this. You need to
represent your classification using the SKOS data model. For some
guidance, see the SKOS Primer [1] and introductory articles [2,3]. An
excellent general introduction to RDF and Linked Data is given for
example in the Linked Data book [4] available for free online. For
specifics on what aspects of SKOS and other RDF vocabularies Skosmos
supports, see the wiki page Data Model [5].

The uriSpace setting is not crucial for Skosmos, this is the least of
your worries. When you represent your data as RDF, the best practice is
to coin a new URI namespace for your data set (see the Linked Data book
for some guidance). Then use that as the value of the uriSpace setting.

-Osma

[1] https://www.w3.org/TR/skos-primer/

[2] http://www.dataversity.net/introduction-to-skos/

[3] http://www.ala.org/alcts/resources/z687/skos

[4] http://linkeddatabook.com/

[5] https://github.com/NatLibFi/Skosmos/wiki/Data-Model

[Sandor Kopacsi]

Dear Osma,
I am using Skosmos version v1.2.1-7-gcf72a45. Should I upgrade it? If yes, which is the most effective way to do that?

Regarding the ÖFOS dataset, you are right, by mistake I sent a wrong file, the structure file was in csv and not in rdf format. 

The rdf file was converted form csv (that I only found), and they are really not SKOS. I will check the documents, you have suggested, and I try to turn them into SKOS format. 

I tried Skomos with the COAR Resource Type Vocabulary, as well, that I have downloaded form http://vocabularies.coar-repositories.org/pubby/page/resource_type as RDF/XML (see attached), and it looks like as a SKOS/RDF file. Previously you said, that COAR uses SKOS XL format (that is not accepted by Skosmos), that is why after uploading it to Fuseki I used the following SPARQL update to convert it to SKOS Core format, as you suggested:

PREFIX skos:   <http://www.w3.org/2004/02/skos/core#> 

PREFIX skosxl: <http://www.w3.org/2008/05/skos-xl#> 

INSERT { 

   ?c skos:prefLabel ?pref . 

   ?c skos:altLabel ?alt . 

   ?c skos:hiddenLabel ?hidden . 

} 

WHERE { 

   { ?c skosxl:prefLabel/skosxl:literalForm ?pref } 

   UNION 

   { ?c skosxl:altLabel/skosxl:literalForm ?alt } 

   UNION 

   { ?c skosxl:hiddenLabel/skosxl:literalForm ?hidden } 

} 

I have set the vocabularies.ttl as follow:

:coarrt a skosmos:Vocabulary, void:Dataset ;

        dc:title "COAR Resource Type Vocabulary - local !"@en ;

        dc:subject :cat_general ;

        skosmos:language "en";

        skosmos:showTopConcepts "true";

        skosmos:loadExternalResources "true";

        skosmos:fullAlphabeticalIndex "true";

        skosmos:arrayClass isothes:ThesaurusArray ;

        void:sparqlEndpoint <http://localhost:3030/ds/sparql> ;

        .

And from Skosmos I got the same Server error message, as in case of ÖFOS:

[Fri Feb 12 15:47:34 2016] [error] [client 131.130.2.250] PHP Fatal error:  Call to a member function getValue() on a non-object in /var/www/skosmos/model/Vocabulary.php on line 146, referer: http://skosmos.phaidra.org/en/?clang=

Is it because I use the wrong version of Skosmos, or should I create a new URI namespace, as you suggested?

Thank you again.

Best Regards,

Sandor

[Osma Suominen]

Dear Sandor,

I think it would be a good idea to upgrade. You may well be experiencing
a bug that has already been fixed. There is always a stable/maintenance
version (currently 1.4) and a development version (currently about to
become 1.5). We provide Skosmos as open source and give limited support
to the community, also because it helps discover problems and collect
new ideas, making the software better overall. But we cannot support
older versions than the most recent ones. New versions are released
usually every 2-3 months or so.

Instructions for upgrading are in the wiki:
https://github.com/NatLibFi/Skosmos/wiki/Upgrading

-Osma

> osma.s...@helsinki.fi <javascript:>
> http://www.nationallibrary.fi

>
> --
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> For more options, visit https://groups.google.com/d/optout.

[Osma Suominen]

Dear Sandor,

It occurred to me that the error is probably caused by the setting
"skosmos:arrayClass isothes:ThesaurusArray". Your vocabulary doesn't
have ThesaurusArrays so the code breaks when trying to query for them.
This was a bug of sorts, it was fixed in Skosmos 1.3 or 1.4 and it no
longer causes an error message.

But just removing this line from the configuration should help, even if
you can't upgrade right now.

-Osma

[Sandor Kopacsi]

Dear Osma,

thank you for your suggestion, but unfortunately it did not help.

In the mean time I could upgrade to Skosmos 1.4. Using the new version I tried with "skosmos:arrayClass isothes:ThesaurusArray" that caused this error-log:

[Wed Feb 17 17:57:53 2016] [error] [client 131.130.2.250] PHP Fatal error:  Uncaught exception 'EasyRdf_Exception' with message 'HTTP request for SPARQL query failed: <html><head><title>Apache Tomcat/7.0.42 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 500 - org.springframework.validation.BeanPropertyBindingResult: 1 errors</h1><HR size="1" noshade="noshade"><p><b>type</b> Exception report</p><p><b>message</b> <u>org.springframework.validation.BeanPropertyBindingResult: 1 errors</u> in /var/www/skosmos/vendor/twig/twig/lib/Twig/Template.php on line 396, referer: http://skosmos.phaidra.org/en/?clang=

and without "skosmos:arrayClass isothes:ThesaurusArray", that caused the same error-log:

[Wed Feb 17 18:05:33 2016] [error] [client 131.130.2.250] PHP Fatal error:  Uncaught exception 'EasyRdf_Exception' with message 'HTTP request for SPARQL query failed: <html><head><title>Apache Tomcat/7.0.42 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 500 - org.springframework.validation.BeanPropertyBindingResult: 1 errors</h1><HR size="1" noshade="noshade"><p><b>type</b> Exception report</p><p><b>message</b> <u>org.springframework.validation.BeanPropertyBindingResult: 1 errors</u> in /var/www/skosmos/vendor/twig/twig/lib/Twig/Template.php on line 396, referer: http://skosmos.phaidra.org/en/?clang=

What else can be wrong?

Thanks again,

Sandor

>> <mailto:skosmos-users+unsub...@googlegroups.com>.

[Osma Suominen]

Dear Sandor,

That's a strange error message. It contains embedded HTML which appears
to come from Tomcat. The Tomcat error message "HTTP Status 500 -
org.springframework.validation.BeanPropertyBindingResult: 1 errors".

Are you running Fuseki inside Tomcat?

Anyway, this appears not to be a Skosmos error, it's your SPARQL
endpoint that is not working.

-Osma

> >> an email to skosmos-user...@googlegroups.com <javascript:>
> >> <mailto:skosmos-user...@googlegroups.com <javascript:>>.

> >> To post to this group, send email to skosmo...@googlegroups.com

> <javascript:>
> >> <mailto:skosmo...@googlegroups.com <javascript:>>.

> >> To view this discussion on the web visit
> >>
> https://groups.google.com/d/msgid/skosmos-users/91b55cad-2c83-4fa6-b62e-bf3aa5d86068%40googlegroups.com
> <https://groups.google.com/d/msgid/skosmos-users/91b55cad-2c83-4fa6-b62e-bf3aa5d86068%40googlegroups.com>
>
> >>
> >>

> <https://groups.google.com/d/msgid/skosmos-users/91b55cad-2c83-4fa6-b62e-bf3aa5d86068%40googlegroups.com?utm_medium=email&utm_source=footer

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>
> >>
> >> For more options, visit https://groups.google.com/d/optout

> <https://groups.google.com/d/optout>.

> >
> >
>
>
> --
> Osma Suominen
> D.Sc. (Tech), Information Systems Specialist
> National Library of Finland
> P.O. Box 26 (Kaikukatu 4)
> 00014 HELSINGIN YLIOPISTO
> Tel. +358 50 3199529
> osma.s...@helsinki.fi <javascript:>
> http://www.nationallibrary.fi
>
> --
> You received this message because you are subscribed to the Google
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> <mailto:skosmos-user...@googlegroups.com>.

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> <mailto:skosmo...@googlegroups.com>.
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[Sandor Kopacsi]

Dear Osma,

I run Fuseki inside Jetty (8.y.z-SNAPSHOT) and not  inside Tomcat. Skosmos uses Apache/2.2.15 (CentOS).

But when I received the "HTTP Status 500 - org.springframework.validation.BeanPropertyBindingResult: 1 errors" message I wanted to access Getty AAT on its remote SPARQL endpoint (http://vocab.getty.edu/sparql), and I just started Skosmos without running my local SPARQL endpoint (Fuseki). 

I assume, that my Fuseki is apparently working, since it works well with Skosmos using the local triple store of Getty AAT, TGN and ULAN as well as the UNESCO Thesaurus in my Fuseki. (I use Fuseki 1.3.1. and  I guess that is it a right version for Skosmos 1.4.)

The previous problem in Vocabulary.php still occurs, when I want to access through Skosmos the remote SPARQL endpoint of Getty AAT (without running the local Fuseki server), or when I want to use Skosmos with the local Fuseki server to use the previously uploaded COAR Resource Type vocabulary (see the attached file which was checked with the Skosify tool), and in both cases I get this error message:

[Thu Feb 18 11:31:02 2016] [error] [client 131.130.2.250] PHP Fatal error:  Call to a member function getValue() on a non-object in /var/www/skosmos/model/Vocabulary.php on line 81, referer: http://skosmos.phaidra.org/en/?clang=

After upgrading Skosmos the getValue() error appears in line 81 and not in 146, as previously, but still generates this Fatal error of Skosmos.

 

I can imagine, that the remote SPARQL endpoint of Getty AAT (and other Getty's) can not be accessed through Skosmos, because they are large and they don't use text index, but I assume the local COAR Resource Type Vocabulary should work. 

What can be wrong?

Thanks again!

Sandor

>      >> <mailto:skosmos-users+unsub...@googlegroups.com <javascript:>>.

>      >> To post to this group, send email to skosmo...@googlegroups.com
>     <javascript:>
>      >> <mailto:skosmo...@googlegroups.com <javascript:>>.
>      >> To view this discussion on the web visit
>      >>
>     https://groups.google.com/d/msgid/skosmos-users/91b55cad-2c83-4fa6-b62e-bf3aa5d86068%40googlegroups.com
>     <https://groups.google.com/d/msgid/skosmos-users/91b55cad-2c83-4fa6-b62e-bf3aa5d86068%40googlegroups.com>
>
>      >>
>      >>
>     <https://groups.google.com/d/msgid/skosmos-users/91b55cad-2c83-4fa6-b62e-bf3aa5d86068%40googlegroups.com?utm_medium=email&utm_source=footer
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>
>      >>
>      >> For more options, visit https://groups.google.com/d/optout
>     <https://groups.google.com/d/optout>.
>      >
>      >
>
>
>     --
>     Osma Suominen
>     D.Sc. (Tech), Information Systems Specialist
>     National Library of Finland
>     P.O. Box 26 (Kaikukatu 4)
>     00014 HELSINGIN YLIOPISTO
>     Tel. +358 50 3199529
>     osma.s...@helsinki.fi <javascript:>
>     http://www.nationallibrary.fi
>
> --
> You received this message because you are subscribed to the Google
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> <mailto:skosmos-users+unsub...@googlegroups.com>.

[Osma Suominen]

Dear Sandor,

You are missing the skosmos:uriSpace setting for COAR.

The line that the error message indicates is this:
https://github.com/NatLibFi/Skosmos/blob/v1.4-maintenance/model/Vocabulary.php#L81

Just set the uriSpace and you should be all right.

-Osma

18.02.2016, 13:45, Sandor Kopacsi kirjoitti:
> Dear Osma,
>

> > >> <mailto:skosmos-user...@googlegroups.com
> <javascript:> <javascript:>>.

> > an email to skosmos-user...@googlegroups.com <javascript:>
> > <mailto:skosmos-user...@googlegroups.com <javascript:>>.

> > To post to this group, send email to skosmo...@googlegroups.com
> <javascript:>
> > <mailto:skosmo...@googlegroups.com <javascript:>>.
> > To view this discussion on the web visit
> >

> https://groups.google.com/d/msgid/skosmos-users/69b8b1be-1bb8-4054-aa0e-5aea249e4539%40googlegroups.com
> <https://groups.google.com/d/msgid/skosmos-users/69b8b1be-1bb8-4054-aa0e-5aea249e4539%40googlegroups.com>
>
> >
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>

> > For more options, visit https://groups.google.com/d/optout
> <https://groups.google.com/d/optout>.
>
>
> --
> Osma Suominen
> D.Sc. (Tech), Information Systems Specialist
> National Library of Finland
> P.O. Box 26 (Kaikukatu 4)
> 00014 HELSINGIN YLIOPISTO
> Tel. +358 50 3199529
> osma.s...@helsinki.fi <javascript:>
> http://www.nationallibrary.fi
>
> --
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