ncbo / ontologies_api

Hypermedia API for NCBO's ontology-related projects
http://data.bioontology.org
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Submissions endpoint fails to return results in AllegroGraph #117

Closed mdorf closed 9 months ago

mdorf commented 1 year ago

When calling the submissions endpoint /submissions in AllegroGraph, an empty set is returned.

mdorf commented 1 year ago

Narrowed the cause down to this SPARQL query that returns data from 4store but no data from AllegroGraph:

SELECT DISTINCT ?id ?released ?creationDate ?homepage ?publication ?documentation ?version ?description ?status ?submissionId ?submissionStatus ?contact ?hasOntologyLanguage ?ontology ?submissionStatus 
FROM <http://data.bioontology.org/metadata/OntologySubmission> 
FROM <http://data.bioontology.org/metadata/Ontology> 
WHERE { 
  ?id a <http://data.bioontology.org/metadata/OntologySubmission> . 
  OPTIONAL { ?id <http://data.bioontology.org/metadata/released> ?released .  } 
  OPTIONAL { ?id <http://omv.ontoware.org/2005/05/ontology#creationDate> ?creationDate .  } 
  OPTIONAL { ?id <http://data.bioontology.org/metadata/homepage> ?homepage .  } 
  OPTIONAL { ?id <http://data.bioontology.org/metadata/publication> ?publication .  } 
  OPTIONAL { ?id <http://omv.ontoware.org/2005/05/ontology#documentation> ?documentation .  } 
  OPTIONAL { ?id <http://omv.ontoware.org/2005/05/ontology#version> ?version .  } 
  OPTIONAL { ?id <http://omv.ontoware.org/2005/05/ontology#description> ?description .  } 
  OPTIONAL { ?id <http://omv.ontoware.org/2005/05/ontology#status> ?status .  } 
  OPTIONAL { ?id <http://data.bioontology.org/metadata/submissionId> ?submissionId .  } 
  OPTIONAL { ?id <http://data.bioontology.org/metadata/submissionStatus> ?submissionStatus .  } 
  OPTIONAL { ?id <http://data.bioontology.org/metadata/contact> ?contact .  } 
  OPTIONAL { ?id <http://omv.ontoware.org/2005/05/ontology#hasOntologyLanguage> ?hasOntologyLanguage .  } 
  OPTIONAL { ?id <http://data.bioontology.org/metadata/ontology> ?ontology .  } 
  OPTIONAL { ?id <http://data.bioontology.org/metadata/submissionStatus> ?submissionStatus .  } 
  OPTIONAL { ?id <http://data.bioontology.org/metadata/ontology> ?internal_join_var_0 .  } 
  OPTIONAL { ?internal_join_var_0 <http://data.bioontology.org/metadata/viewOf> ?internal_join_var_1 .  } 
  FILTER(!BOUND(?internal_join_var_1))
}

When the line FILTER(!BOUND(?internal_join_var_1)) is removed/commented out, the query returns expected results (which now include Ontology Views)

mdorf commented 1 year ago

Franz patch spr46041-v7.3.1.fasl.patch resolves this issue. The patch will also be rolled into the AllegroGraph v7.4 release.