RDF Extension Reconciliation not working with DBpedia

[kim vella]

I am using open-refine 2.8 with RDF extension when I am trying to reconcile a column from my dataset (CSV uploaded dataset) with dbpedia the reconciliation process hangs on the working screen.

I am trying to use the English SPARQL endpoint. I have also tried using the Spanish SPARQL endpoint the results are the same. 

Below is a sample of the dataset, I am trying to reconcile with the provider column: 

ONS AREA ID (2)

SHA NAME

ODS CODE (3)

PROVIDER

E18000004	EAST MIDLANDS	RFS	CHESTERFIELD ROYAL HOSPITAL NHS FOUNDATION TRUST
E18000004	EAST MIDLANDS	RTG	DERBY HOSPITALS NHS FOUNDATION TRUST
E18000004	EAST MIDLANDS	RNQ	KETTERING GENERAL HOSPITAL NHS FOUNDATION TRUST

[fadi maali]

Hello Kim

The RDF extension doesn't work with Openrefine 2.8 at the moment. I am working in that. I should have an alpha version in a week approx.

You might try this (I haven't tried it myself):

https://github.com/pbackx/grefine-rdf-extension/releases 

Regards,

Fadi

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[kim vella]

Hi Fadi,

Thank you for your quick reply I will check and test it and get back to you.

Best Regards,

Kim Vella

[kim vella]

Hi Fadi,

I tried using that extension and it is giving me the following error do you know how I can solve it? In the meantime, I will try using LODRefine.

HTTP ERROR 500

Problem accessing /project. Reason:

    Butterfly Error
Butterfly incurred in the following errors while initializing:
java.lang.Exception: Failed to initialize module rdf-extension [edu.mit.simile.butterfly.ButterflyModuleImpl]
	at edu.mit.simile.butterfly.Butterfly.initializeModule(Butterfly.java:478)
	at edu.mit.simile.butterfly.Butterfly.configure(Butterfly.java:451)
	at edu.mit.simile.butterfly.Butterfly.init(Butterfly.java:308)
	at org.mortbay.jetty.servlet.ServletHolder.initServlet(ServletHolder.java:440)
	at org.mortbay.jetty.servlet.ServletHolder.doStart(ServletHolder.java:263)
	at com.google.refine.RefineServer.configure(Refine.java:296)
	at com.google.refine.RefineServer.init(Refine.java:208)
	at com.google.refine.Refine.init(Refine.java:114)
	at com.google.refine.Refine.main(Refine.java:108)
Caused by: org.mozilla.javascript.EvaluatorException: Can't find method com.google.refine.RefineServlet.cacheClass(object). (file:/F:/ProgramFiles/openrefine-2.8/webapp/extensions/grefine-rdf-extension-0.9.0.1/module/MOD-INF/controller.js#82)
	at org.mozilla.javascript.DefaultErrorReporter.runtimeError(DefaultErrorReporter.java:109)
	at org.mozilla.javascript.Context.reportRuntimeError(Context.java:938)
	at org.mozilla.javascript.Context.reportRuntimeError(Context.java:994)
	at org.mozilla.javascript.Context.reportRuntimeError1(Context.java:957)
	at org.mozilla.javascript.NativeJavaMethod.call(NativeJavaMethod.java:166)
	at org.mozilla.javascript.optimizer.OptRuntime.call1(OptRuntime.java:66)
	at org.mozilla.javascript.gen.c6._c4(file:/F:/ProgramFiles/openrefine-2.8/webapp/extensions/grefine-rdf-extension-0.9.0.1/module/MOD-INF/controller.js:82)
	at org.mozilla.javascript.gen.c6.call(file:/F:/ProgramFiles/openrefine-2.8/webapp/extensions/grefine-rdf-extension-0.9.0.1/module/MOD-INF/controller.js)
	at org.mozilla.javascript.ContextFactory.doTopCall(ContextFactory.java:398)
	at org.mozilla.javascript.ScriptRuntime.doTopCall(ScriptRuntime.java:3065)
	at org.mozilla.javascript.gen.c6.call(file:/F:/ProgramFiles/openrefine-2.8/webapp/extensions/grefine-rdf-extension-0.9.0.1/module/MOD-INF/controller.js)
	at edu.mit.simile.butterfly.ButterflyModuleImpl.scriptInit(ButterflyModuleImpl.java:636)
	at edu.mit.simile.butterfly.ButterflyModuleImpl.init(ButterflyModuleImpl.java:94)
	at edu.mit.simile.butterfly.Butterfly.initializeModule(Butterfly.java:476)
	... 8 more

[Stuart Kenny]

Hi, I've tested DBpedia reconciliation using my fork of the RDF extension: https://github.com/stkenny/grefine-rdf-extension/tree/orefine

It is working with my fork of OpenRefine 2.8: https://github.com/stkenny/OpenRefine/tree/rdf-extension

The introduction of the Xerces-J jars into OpenRefine caused at least some of the problems. The fork above removes those.

Regards,

Stuart.

[kim vella]

Hi Stuart,

I tried installing the openrefine from that fork and I managed to reconcile with wiki data but not with DBpedia, now I am trying to build the RDF extension taken from: https://github.com/stkenny/grefine-rdf-extension/tree/orefine

and this error is being given when mvn clean compile is being executed:

Could not resolve dependencies for project nl.dtls:grefine-rdf-extension:jar:1.0.0-SNAPSHOT: Failure to find org.openrefine:openrefine:jar:2.8 in https://dev-iesl.cs.umass.edu/nexus/content/repositories/releases/

Do you know how I can resolve these issues, please?

Best Regards,

Kim Vella 

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[Stuart Kenny]

Hi, yes, you need to have the jar file in your local Maven repository. You can follow the instructions here: https://github.com/DTL-FAIRData/openrefine-maven-shim#usage

Change the version 2.7 to 2.8 in the commands, and in the pom.xml, and it should work.

Regards,

Stuart.

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[kim vella]

Hi Stuart,

I am trying to produce a jar file for the open-refine from the fork you gave me to no avail, is there a right way to do this (I am using open refine on a windows machine)? 

I have also tried to produce a jar file directly from eclipse and also used the openrefine-2.8-server.jar. When I use the maven install to install the open-refine jar file just produced to the maven repository it seems that the openrefine jar is installed, but when I try to use maven compile to produce the rdfextension folder, the resulting zipped folder contains only the module folder. Therefore when I try to put this folder to the openrefine extension folder, it does not consider it as a valid extension. 

Thank you for your patience

Best Regards,

Kim Vella

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[Stuart Kenny]

Hi, so does your extensions directory look something like:

extensions

     |_rdf-extension

              |_module

That should be all you need. Is there a specific error you are seeing?

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[kim vella]

Hi Stuart,

Yes that's what I have but when I open OpenRefine there is no RDF extension drop down next to the extension label. I used to use this in OpenRefine 2.6 to change the template of the RDF.

Was this moved to somewhere else?

If I needed to add another reconciliation service I would do that from Reconcile -> Start Reconciling->Add Standard Service? 

extensions

     |_rdf-extension

              |_module

                  |_images

                  |_MOD_INF

                  |_scripts

                  |_styles

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[Stuart Kenny]

Hi, haven't been able to reproduce this unfortunately. I was having a problem like this caused by an error in the database extension javascript that prevented the module from being loaded, but the rdf-extension branch of the forked OpenRefine repo has a fix for that. Are there any errors in the javascript console when you open a project? The RDF extension drop down should be available as before if everything was working.

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[Stuart Kenny]

Hi, further to below I've tried building distributions that include a working RDF extension. You can find them here: https://github.com/stkenny/OpenRefine/releases/tag/2.8-rdf.1

It's difficult for me to test the Windows version fully, but on a Windows 8 VM with JRE 8 it seems to be working. Might help you if compiling isn't working out.

Regards,

Stuart.

[kim vella]

Hi Stuart,

That distribution worked perfectly!!! A+ support. 

Thank you for your time and your patience. 

Best Regards,

Kim Vella 

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