Using GraphDB Free with VB3

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Roland Wingerter

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Jan 15, 2018, 10:43:04 AM1/15/18
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Hello all,

I need some guidance on how to create a new VB3 project using GraphDB as triple store.

I have downloaded and installed GraphDB Free on my local machine. In GraphDB, I have created a new empty repository and set it as the default repository ( repository URL http://192.168.2.103:7200/repositories/VocBench_00).

Here is my input in the VB3 "Create project" screen.

Repository Access: "CreateRemote"
- Server URL http:192.168.2.103
- Username & Password: (default credentials).

Configuration "GraphDB Free (remote only)"
- baseURL  www.my.com
- defaultNS  myNamespace

When I click "Create" I get this error message: "Error - could not read protocol version from server: org.eclipse.rdf4j.repository.RepositoryException".

Here are the repository details in GraphDB:
- Repository ID* "VocBench_00"
- baseURL: http://example.org/owlim#

Please can anyone give me some guidance on this?

Regards
Roland




Armando Stellato

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Jan 16, 2018, 10:43:16 AM1/16/18
to Roland Wingerter, vocbench-user

Dear Roland,

 

Sorry for keeping you waiting, but since in the past days I created some test-drive pages for VB3, after your email of yesterday I planned to write a specific test-drive for GraphDB, enabling all of VB features. I just replied to Bart Leeuwen (who posted a similar issue just now) by providing this link:

 

http://vocbench.uniroma2.it/doc/user/test_drive.jsf#creating_a_skos_project_for_managing_a_large_thesaurus_by_connecting_to_an_external_triple_store__exploiting_history__validation_and_inference_

 

as for Bart’s case, I think the “failed to get server protocol” exception is thrown by RDF4J also when the server cannot be found at all..

 

In your specific case, it seems you omitted the port of the triple store server (unless you explicitly changed the port of GDB to 80). Also, if both GDB and VB/ST are on the same machine (strictly speaking, it suffices for ST to be on the same machine of GDB), you can set http://localhost:7200 as the server address.

 

Another aspect: there is no need to prepare a repository on GDB, VB3 is able to create the repository (or the repositories if you using one or both of History and Validation) remotely when the project is being created.

 

There could be other issues in your configuration, but you might want to look at the test-drive above (that should work if the conditions are respected) and later start to play around with further configurations

 

Cheers,

 

Armando

 

 

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Roland Wingerter

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Jan 16, 2018, 5:57:23 PM1/16/18
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Dear Armando,

the EUROVOC "test drive" is exactly what I needed! Thank you for your great support, which is very much appreciated.

So far I could only follow through part of the test drive but things look very promising.

It looks like the "test drive" document contains two broken links:
1. The link to instructions on the sail component: "Follow the instructions for doing that in the related section of the system administration manual" 
2. The link in "Download the Eurovoc thesaurus RDF file and unzip it."

I found the section on the the change-tracking sail component and dropped the jar file in GraphDB's lib directory ("C:\Users\...\AppData\Local\GraphDB Free\app\lib") as requested. However, when clicked on the "Create" button to create the project and the repositories on GraphDB I got the following error message:

>>it.uniroma2.art.semanticturkey.exceptions.ProjectUpdateException: org.eclipse.rdf4j.repository.RepositoryException: org.eclipse.rdf4j.repository.config.RepositoryConfigException: Unsupported Sail type: http://semanticturkey.uniroma2.it/sail/changetracker
Details: it.uniroma2.art.semanticturkey.exceptions.ProjectAccessException
<<

I tried several times, but the problem did not go away. However things worked fine when I created the project without "History" and "Validation". Is there anything I can check?

Thanks once again.

Kind regards
Roland

Armando Stellato

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Jan 17, 2018, 6:25:47 AM1/17/18
to Roland Wingerter, vocbench-user

Dear Roland,

 

I noticed the first broken link and was going to fix while was almost sure I tested the RDF file link (I happened to miss the http:// at the start), so thanks for spotting them! Fixed now.

 

Going back to your case, from your report it seems you are using Windows and from the path you mentioned you probably used the desktop installation. I’m not familiar with the desktop installation (on the standalone version of GDB there’s just a lib folder inside the root of the application).

Two possibilities come to my mind:

·         It’s not the proper lib directory (isn’t GDB installed under “Programs” ?). The fact that there is a “app” directory inside the “…\AppData\GraphDB Free” makes me think that everything is there though

·         Did you put the jar without turning the server off and on? I suppose hot-plug doesn’t work…

 

Cheers,

 

Armando

 

 

From: vocben...@googlegroups.com [mailto:vocben...@googlegroups.com] On Behalf Of Roland Wingerter
Sent: Tuesday, January 16, 2018 11:57 PM
To: vocbench-user <vocben...@googlegroups.com>
Subject: {Disarmed} Re: [vocbench-user] Using GraphDB Free with VB3

 

Dear Armando,

the EUROVOC "test drive" is exactly what I needed! Thank you for your great support, which is very much appreciated.

So far I could only follow through part of the test drive but things look very promising.

It looks like the "test drive" document contains two broken links:
1. The link to instructions on the sail component: "Follow the instructions for doing that in the related section of the system administration manual" 
2. The link in "Download the Eurovoc thesaurus RDF file and unzip it."

I found the section on the the change-tracking sail component and dropped the jar file in GraphDB's lib directory ("C:\Users\...\AppData\Local\GraphDB Free\app\lib") as requested. However, when clicked on the "Create" button to create the project and the repositories on GraphDB I got the following error message:

>>it.uniroma2.art.semanticturkey.exceptions.ProjectUpdateException: org.eclipse.rdf4j.repository.RepositoryException: org.eclipse.rdf4j.repository.config.RepositoryConfigException: Unsupported Sail type: http://semanticturkey.uniroma2.it/sail/changetracker
Details: it.uniroma2.art.semanticturkey.exceptions.ProjectAccessException
<<

I tried several times, but the problem did not go away. However things worked fine when I created the project without "History" and "Validation". Is there anything I can check?

Thanks once again.

Kind regards
Roland


Am Dienstag, 16. Januar 2018 16:43:16 UTC+1 schrieb Armando Stellato:

Dear Roland,

 

Sorry for keeping you waiting, but since in the past days I created some test-drive pages for VB3, after your email of yesterday I planned to write a specific test-drive for GraphDB, enabling all of VB features. I just replied to Bart Leeuwen (who posted a similar issue just now) by providing this link:

 

 

as for Bart’s case, I think the “failed to get server protocol” exception is thrown by RDF4J also when the server cannot be found at all..

 

In your specific case, it seems you omitted the port of the triple store server (unless you explicitly changed the port of GDB to 80). Also, if both GDB and VB/ST are on the same machine (strictly speaking, it suffices for ST to be on the same machine of GDB), you can set http://localhost:7200 as the server address.

 

Another aspect: there is no need to prepare a repository on GDB, VB3 is able to create the repository (or the repositories if you using one or both of History and Validation) remotely when the project is being created.

 

There could be other issues in your configuration, but you might want to look at the test-drive above (that should work if the conditions are respected) and later start to play around with further configurations

 

Cheers,

 

Armando

 

 

From: vocben...@googlegroups.com [mailto:vocben...@googlegroups.com] On Behalf Of Roland Wingerter
Sent: Monday, January 15, 2018 4:43 PM
To: vocbench-user <vocben...@googlegroups.com>
Subject: [vocbench-user] Using GraphDB Free with VB3

 

Hello all,

I need some guidance on how to create a new VB3 project using GraphDB as triple store.

I have downloaded and installed GraphDB Free on my local machine. In GraphDB, I have created a new empty repository and set it as the default repository ( repository URL MailScanner warning: numerical links are often malicious: http://192.168.2.103:7200/repositories/VocBench_00).


Here is my input in the VB3 "Create project" screen.

Repository Access: "CreateRemote"
- Server URL http:192.168.2.103
- Username & Password: (default credentials).

Configuration "GraphDB Free (remote only)"
- baseURL  www.my.com
- defaultNS  myNamespace

When I click "Create" I get this error message: "Error - could not read protocol version from server: org.eclipse.rdf4j.repository.RepositoryException".

Here are the repository details in GraphDB:
- Repository ID* "VocBench_00"
- baseURL: http://example.org/owlim#

Please can anyone give me some guidance on this?

Regards
Roland


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Armando Stellato

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Jan 17, 2018, 6:32:38 AM1/17/18
to Roland Wingerter, vocbench-user

Sorry maybe I was not clear with the first hypothesis: I meant to say that the fact that there is a “app” directory means that the application is really there, separated from the data exactly by that folder


- defaultNS  myNamespace

When I click "Create" I get this error message: "Error - could not read protocol version from server: org.eclipse.rdf4j.repository.RepositoryException".

Here are the repository details in GraphDB:
- Repository ID* "VocBench_00"



Please can anyone give me some guidance on this?

Regards
Roland

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Roland Wingerter

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Jan 17, 2018, 10:14:40 AM1/17/18
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Dear Armando,

yes my OS is Windows. The GraphDB installation path is correct according to the GraphDB documentation: http://graphdb.ontotext.com/documentation/standard/configuring-graphdb.html.

There are two lib directories under ...\AppData\Local\GraphDB Free\ :
- app\lib
- runtime\lib

I copied "st-changetracking-sail-2.0.jar" into both of them and into the \app\ directory as well. I restarted GraphDB and Vocbench, but the error message does not go away. This is not a problem however, since for the time being I can do without history and validation.

Kind regards
Roland

Armando Stellato

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Jan 17, 2018, 5:51:24 PM1/17/18
to Roland Wingerter, vocbench-user

Dear Roland,

 

I will look into it. I never downloaded the GraphDB Windows desktop installation as I preferred to keep my registry clean from it and always used the standalone version (u need java installed, but u already have if you are using VB3 ;-) ).

 

In the meanwhile, two possibilities if you ever need to use H&V:

 

  • Download the standalone server of GDB (proved to work)
  • Pls check if GDB is under “Programs Files” or “Program Files (x86)”. The link you reported clearly mentions that the one under AppData is the home directory (which is for the data and not the application), while for the standalone it says that the default home is the same as the distribution directory. If there GDB under any of the two Programs directories, then it’s under its lib directory that you need to drop the change-tracking sail jar

 

Cheers,

 

Armando

 

 

 


- defaultNS  myNamespace

When I click "Create" I get this error message: "Error - could not read protocol version from server: org.eclipse.rdf4j.repository.RepositoryException".

Here are the repository details in GraphDB:
- Repository ID* "VocBench_00"



Please can anyone give me some guidance on this?

Regards
Roland

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Roland Wingerter

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Jan 18, 2018, 7:03:53 AM1/18/18
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Dear Armando,

it is good to know that H&V works with the GraphDB standalone version. I will download and install it.

On my computer, there is definitely no GraphDB under “Program Files” and “Program Files (x86)”.

Thank you very much.

Kind regards
Roland

Roland Wingerter

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Jan 18, 2018, 5:08:10 PM1/18/18
to vocbench-user
Dear Armando,

with the standalone version of GraphDB Free I was able to create the project with History and Validation.

I started the data import at 17:30 and at 19:00 VB3 was still "Loading", while the GDB window displayed this error message:

[ERROR] 2018-01-18 18:04:47,752 [http-nio-7200-exec-6 | c.o.f.r.GraphdbRepositor
iesService] Couldn't get size from sail repository. class it.uniroma2.art.semant
icturkey.changetracking.sail.ChangeTracker

After shutting down Karaf, GraphDB and closing the browser windows with VB3 and GraphDB I restarted everything. Opening the EUROVOC project I can see the data. A Sparql COUNT(*) reports 2,158,624 triples.

So the import worked, except that
- there was this GraphDB error message and I can't be sure that the import was complete
- GraphDB does not display the usual information about the repository size (no. of statements etc).

My notebook has a dual core i5 cpu and 8 GB memory. During import the memory usage was at 90%.

Kind regards
Roland

Armando Stellato

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Jan 19, 2018, 4:56:54 AM1/19/18
to Roland Wingerter, vocbench-user

Dear Roland,

 

Glad the H&V worked for you. I’ll ask the OntoText guys about the proper lib folder of the desktop distribution.

 

The slow loading issue seems related to some problem with GraphDB and might be due to available memory and other factors. GDB stores everything on HD, but RAM is used for caching and other processes which might require to work in-memory with large quantities of data, especially with reasoning on.

I previously was able to load it in acceptable time (bunch of minutes, don’t recall exactly) with my previous laptop, which is pretty much your same configuration (Surface 2, i5 4300, 8Gb memory, it had SSD, not sure yours, and it might affect a little), however it also depends on how much free-memory you had at the moment.

 

Anyway, glad in the end the data was loaded. I made a count on another version we had on our sandbox and it reports: 2158656, but very much like we had played a little with it, so I guess you have all the triples.

 

In general, two things that require quite lot of processing on large datasets are:

  • Inference. From the test-drive you followed, if you remove the reasoner (it suffices not to specify the inference level in the sail configuration) loading will be much faster
  • History: the first time you load a repo, if you have history, it will put all of its triples in the history, taking quite some time to expand each of them into reified triples to be added to the commit action.
  • Validation: this means that all of the triples are “parked” in the staging graph, and then need to be validated. However, if you ticked the “skip validation” option (it is mentioned in the test-drive) this step is being skipped. This option is available only to administrators and project managers, other users would need by first to be authorized to perform a “load”, and then would have to pass through the validation. But this is normal, such large data imports are usually associated to the first setup of a project which starts over an already existing large repository

 

Cheers,

 

Armando

 

 

 

 

 

 

 

>>it.uniroma2.art.semanticturkey.exceptions.ProjectUpdateException: org.eclipse.rdf4j.repository.RepositoryException: org.eclipse.rdf4j.repository.config.RepositoryConfigException: Unsupported Sail type: MailScanner ha rilevato un possibile tentativo di frode proveniente da "eur02.safelinks.protection.outlook.com" http://semanticturkey.uniroma2.it/sail/changetracker

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Roland Wingerter

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Jan 19, 2018, 5:36:45 AM1/19/18
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Dear Armando,

thank you very much for the additional information.

Kind regards
Roland

Sylwia Oz

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Aug 1, 2018, 4:44:11 AM8/1/18
to vocbench-user
Dear Armando,

I was just wondering if there is a follow-up regarding the desktop distribution of graphDB and the H&V issue Roland logged in. I have the same problem right now so I was just wondering if a solution has been found.

Kind regards
Sylwia

Armando Stellato

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Aug 1, 2018, 5:11:33 AM8/1/18
to Sylwia Oz, vocbench-user

Dear Sylwia,

 

There was no follow up as the main issue was resolved. The solution is to use the standalone version. Other issues reported did not appear anymore on future interactions with Roland (so probably some issue happened once)

 

A couple of question:

 

  • could you tell me the version of GDB you are using? Maybe a new version is out and has some incompatibilities (in case I will download it and test it myself).
  • Since there were more issues reported in this thread, could you pls report the issue you are having and the text of the exception you are getting?

 

Also, to avoid issues piling up: concerning your previous msg of yesterday, was the issue resolved?

 

Cheers,

 

Armando

 

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Sylwia Oz

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Aug 1, 2018, 8:18:03 AM8/1/18
to vocbench-user
Thank you for getting back to me. The issue I logged yesterday is resolved as I managed to connect to VocBench local host.

Regarding my current issue:

I am using GDB free 8.6.1 (windows)

When I check H&V options, I get the following message:


Besides that, I followed the test drive instructions. I was able to load Eurovoc and Wordnet wn_08_eng.rdf but not pwn-concepts.rdf (I interrupted the process after a time lapse of 2 hours).

Kind regards
Sylwia

Armando Stellato

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Aug 1, 2018, 9:28:52 AM8/1/18
to Sylwia Oz, vocbench-user

Dear Sylwia,

 

Glad you solved the first issue.

 

Concerning your recent issue, a few notes:

 

  • It seems to me you have not deployed the change-tracking sail inside GDB before running it, as described here: http://vocbench.uniroma2.it/doc/sys/#separate_triple_store
  • Or, maybe you have deployed it but it is not seen by GDB. You say you are using the 8.6.1 (windows). The OS specific versions are reported to have issues in dynamically loading the change-tracking sail lib. You could simply download the stand-alone server version of GDB (it is available for download together with the OS-Specific packages from the email Ontotext has sent you with the download links). That version requires only java to be installed in order to be run.

 

However, I just tested GDB 8.6.1 and I see that, due to the adoption of a new version of the RDF4J library and to a backward-incompatibility issue, the new version is not compatible with the st-changetracking sail

 

So, I am contacting Ontotext in order to solve the last point (get at least a download link to past versions of the GDB triplestore). I gave you in any case the previous indications because I see from the error above that you had other kind of problems that need to be solved as explained in the two itemized points above.

 

I’ll be also sending a message in list telling all past users not to update to GDB 8.6.x

 

Thanks for spotting this,

 

Armando

 

 

 

 

From: vocben...@googlegroups.com <vocben...@googlegroups.com> On Behalf Of Sylwia Oz
Sent: Wednesday, August 1, 2018 2:18 PM
To: vocbench-user <vocben...@googlegroups.com>
Subject: {Disarmed} Re: {Disarmed} Re: {Disarmed} Re: {Disarmed} Re: {Disarmed} Re: [vocbench-user] Using GraphDB Free with VB3

 

Thank you for getting back to me. The issue I logged yesterday is resolved as I managed to connect to VocBench local host.

 

Regarding my current issue:

 

I am using GDB free 8.6.1 (windows)

 

When I check H&V options, I get the following message:

https://lh3.googleusercontent.com/-SDIc183MrS4/W2GkAJ1ntNI/AAAAAAAAAY0/x4fYEcgUCgALHa-qCba3TDD478fNbHM6gCLcBGAs/s320/error4.PNG

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Sylwia Oz

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Aug 3, 2018, 11:00:48 AM8/3/18
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Dear Armando,

I deployed the change tracking sail inside GDB so probably  it is not seen.

I will try the stand alone server version.

Thanks a lot for your help and have a good weekend!
Sylwia

Armando Stellato

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Aug 3, 2018, 12:02:13 PM8/3/18
to Sylwia Oz, vocbench-user

Dear Sylwia,

 

If it was not the standalone-server version, then it’s surely like this (we have already tested this).

Pls remember to download GDB 8.5 (from the link I provided yesterday) instead of 8.6.1

Have a nice weekend,

Armando

 

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