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Fix restrictions for nested level of someValuesFrom (depth 4) and improve restrictions definition for non legacy schema

Nicola Stoira requested to merge sphnc-459 into main
  • Recursive call to method for extracting nested restrictions from someValuesFrom
  • Update SHACLer and SPARQLer commits (STILL to be updated once changes for these tools are merged) --> SHACLer done
  • For non legacy (ONLY) schema, update the get_restrictions_map method to also include the class in range in the path, e.g.
{
"https://biomedit.ch/rdf/sphn-schema/sphn#SingleNucleotideVariation[sphnSingleNucleotideVariation]https://biomedit.ch/rdf/sphn-schema/sphn#hasChromosomalLocation[sphnChromosomalLocation]https://biomedit.ch/rdf/sphn-schema/sphn#hasChromosome": [
        "https://biomedit.ch/rdf/sphn-schema/sphn#Chromosome"
    ]
}

this allows to extract restrictions at lower level.

  • JSON schema and database table slightly change for SPHN only. Additional UCUM enum values are now listed and defined into new data types for the database columns
  • For non legacy schemas, the restrictions map is extracted recursively. This mean that if we reach a concept that it already defined in the restrictions map we include all it's properties in the original source concept
  • Special logic that was initially introduced for 2023.2 sphn:AccessDevicePresence/sphn:hasMedicalDevice being restricted to sphn:MedicalDevice is now executed only for legacy schemas
Edited by Nicola Stoira

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