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JervenBolleman / void-generator

Calculate statistics for use in a Service Description or Void file
MIT License
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Error in URIs generated and `sd:enpoint` object when processing WikiPathways #5

Open vemonet opened 6 months ago

vemonet commented 6 months ago

Hi, I have tried to run it on WikiPathways SPARQL endpoint but I am facing some minor issues

I ran it with the following command:

java -jar target/void-generator-*.jar -r https://sparql.wikipathways.org/sparql --void-file void-wikipath.ttl --iri-of-void https://void -g http://rdf.wikipathways.org/

It manages to generates stats, but the URI for the void objects seems to be off, we are getting URIs with exclamation marks instead of forward slashes, e.g. <https://voidrdf.wikipathways.org!0d30180e88607a9b9f3e7efdf6a5a920!homepage>

And the URI used for the sd:endpoint is the VOID URI, when I would expect it to be the URI of the SPARQL endpoint I gave in input:

<https://void> rdf:Property sd:Service;
  sd:defaultDataset _:0;
  sd:endpoint <https://void>;
JervenBolleman commented 5 months ago

Hi @vemonet

You are right. This again was an UniProt assumption that infected the code. A new option -p or ----public-repository is added to set the service description location/which is the endpoint. This is different than -r as this project might be run on an internal not yet published endpoint.

java -jar target/void-generator-*.jar -r https://sparql.wikipathways.org/sparql \
   -p https://sparql.wikipathways.org/sparql \
   --void-file void-wikipath.ttl \
   --iri-of-void 'https://rdf.wikipathway.org/.well-known/void#' \
    -g http://rdf.wikipathways.org/