Deleting blank nodes

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Benjamin Gross

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Jan 18, 2017, 2:33:32 PM1/18/17
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Does anyone have any advice on how to remove blank nodes?
I used a SPARQL construct query to get all the blank nodes. I tried using Harvester in —modeRemove against the graphs with the blank nodes, but it doesn’t seem to have any effect.

All the blank nodes seem to be related to the rdf files loaded by VIVO. I’ve always just ignored them, but when trying to start up VIVO using the latest code on the develop branch I get the message
2017-01-17 15:32:12,711 INFO [FileGraphSetup] Updating /usr/local/vivo-test/home/rdf/abox/filegraph/academicDegree.rdf because graphs are not isomorphic
2017-01-17 15:48:33,695 INFO [FileGraphSetup] dbModel: 454 ; fileModel: 454

and startup hangs. Graham speculated blank nodes might be to blame. Any ideas?

Benjamin

Brian Lowe

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Jan 18, 2017, 2:46:27 PM1/18/17
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Hi Benjamin,

I don't know whether the behavior has been changed recently, but it at least used to be that blank node structures could be deleted normally through VIVO's RDFService (that is, any deletion being done through VIVO rather than directly against the triple store). The RDFService should convert the blank node labels into corresponding variables in query patterns whose matching triples are then removed.

If you're using the Harvester directly against the triple store, you won't get this extra fuctionality. That said, I can't think of any reason why the academicDegree.rdf file should have any blank nodes. (Usually they occur -- by necessity -- only in ontology files that include things like restrictions and other anonymous classes.)

Brian
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Benjamin Gross

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Jan 18, 2017, 5:29:45 PM1/18/17
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Hi Brian,
Thanks for the insight on the creation of blank nodes for ontology files. I agree, I don’t actually see any blank nodes related to the academicDegree.rdf file. I deleted the file on a lark and unfortunately it still hangs. The last line in the log is now INFO [RDFFilesLoader] Loading rdf/auth/everytime/permission_config.n3 so I wonder if the real issue is with whatever comes after RDFFilesLoader (FileGraphSetup?). Thought maybe it was a permissions issue but can’t see anything wrong there. Tried a build without our custom installer and same issue. Tried removing the new turtle logic line in the java file, no better. If I use a blank database it starts up fine, so I can continue development, but this will be a problem in the future unless I can figure out the issue. Stuck for now...

Benjamin
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