"ERROR: You have attempted to upload invalid data" when uploading a turtle file

turtle
virtuoso
#1

I have a ttl file that I want to load in virtuoso triplestore, I used Quad Store Upload in the UI, the file didn’t load succefully and this error was shown:

You have attempted to upload invalid data. You can only upload RDF, Turtle, N3 serializations of RDF Data to the RDF Data Store.

After investigating I got a sample that causes it

@prefix bkr:  <http://www.ondex.org/bioknet/resources/> .
@prefix rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bk:  <http://www.ondex.org/bioknet/terms/> .
@prefix dc:  <http://purl.org/dc/elements/1.1/> .

bkr:phenotype_52049  rdf:type  bk:Phenotype ;
        dc:identifier  bkr:accsn_arapheno_altered_nonphotochemical_quenching_of_chlorophyll_fluorescence__unable_to_convert_violaxanthin_to_zeaxanthin_in_excessive_light_via_the_xanthophyll_cycle__affects_the_structural_gene_encoding_violaxanthin_deepoxidase__exhibits_greatly_reduced_nonphotochemical_quenching__demonstrating_that_violaxanthin_deepoxidation_is_required_for_the_bulk_of_rapidly_reversible_nonphotochemical_qenching__altered_regulation_of_photosynthetic_energy_conversion_is_associated_with_increased_sensitivity_to_photoinhibition_ .

bkr:accsn_arapheno_altered_nonphotochemical_quenching_of_chlorophyll_fluorescence__unable_to_convert_violaxanthin_to_zeaxanthin_in_excessive_light_via_the_xanthophyll_cycle__affects_the_structural_gene_encoding_violaxanthin_deepoxidase__exhibits_greatly_reduced_nonphotochemical_quenching__demonstrating_that_violaxanthin_deepoxidation_is_required_for_the_bulk_of_rapidly_reversible_nonphotochemical_qenching__altered_regulation_of_photosynthetic_energy_conversion_is_associated_with_increased_sensitivity_to_photoinhibition_
        rdf:type            bk:Accession .

The error disappear when I replaced accsn_arapheno_altered_nonphotochemical_quenching_of_chlorophyll_fluorescence__unable_to_convert_violaxanthin_to_zeaxanthin_in_excessive_light_via_the_xanthophyll_cycle__affects_the_structural_gene_encoding_violaxanthin_deepoxidase__exhibits_greatly_reduced_nonphotochemical_quenching__demonstrating_that_violaxanthin_deepoxidation_is_required_for_the_bulk_of_rapidly_reversible_nonphotochemical_qenching__altered_regulation_of_photosynthetic_energy_conversion_is_associated_with_increased_sensitivity_to_photoinhibition_ with a shorter string … so I understood that the lenght of the predicate was the cause.

Is there a way to avoid this without modifying the ttl files?

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#2

If you use the Virtuoso trace_on() function to enable additional tracing of Virtuoso server activities to the “virtuoso.log” file you will see the error:

ERRS_0 37000 SP029 TURTLE RDF loader, line 7: qualified URI contains abnormally long 'local part' after the colon at bkr:accsn_arapheno_altered_nonphotochemical_quenching_of_chlorophyll_fluorescence__unable_to_convert_violaxanthin_to_zeaxanthin_in_excessive_light_via_the_xanthophyll_cycle__affects_the_structural_gene_encoding_violaxanthin_deepoxidase__exhibits_greatly_reduced_nonphotochemical_quenching__demonstrating_that_violaxanthin_deepoxidation_is_required_for_the_bulk_of_rapidly_reversible_nonphotochemical_qenching__altered_regulation_of_photosynthetic_energy_conversion_is_associated_with_increased_sensitivity_to_photoinhibition_

Thus is appears you have exceeded the limit on the length of the local part of a URI, thus will need to check with development what the limit is.

Do you have a specific need for URIs with such long local parts ?

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#3

Thank you for your reply, actually I’m not the one who generate the data, I would prefer to leave the file as it is (if there is a way to avoid this issue of course) otherwise I’ll have to contact the providers.

I thought that maybe there is a way to change the limit in the configuration or something like that.

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#4

Development indicate there is a 512K limit on the length of the local part of a URI and the length of your above is 522 chars hence the error. This is not a configurable limit, although development indicate they could consider if it is possible to increasing the length or making in configurable.

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#5

OK, I’ll contact the providers to let them know.
Thank you again!

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