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TopQuadrant / shacl

SHACL API in Java based on Apache Jena
Apache License 2.0
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SHACL focus node & source Shape #88 #160

Closed ensaremirerol closed 10 months ago

ensaremirerol commented 10 months ago

88

Basically added a extra flag for CLI tool named -addBlankNodes. With this flag enabled tool will append all blank nodes that references shapes file.

Here is the data/shape file I used in testing and the validation report outputted from tool with mention flag enabled

Data and Shape

@prefix : <https://biomedit.ch/rdf/sphn-schema/sphn#> .
@prefix chop: <https://biomedit.ch/rdf/sphn-resource/chop/> .
@prefix constraints: <https://biomedit.ch/rdf/sphn-schema-constraints/sphn#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix eco: <http://purl.obolibrary.org/obo/ECO_> .
@prefix edam: <http://edamontology.org/> .
@prefix efo: <http://www.ebi.ac.uk/efo/EFO_> .
@prefix emdn: <https://biomedit.ch/rdf/sphn-resource/emdn/> .
@prefix genepio: <http://purl.obolibrary.org/obo/GENEPIO_> .
@prefix geno: <http://purl.obolibrary.org/obo/GENO_> .
@prefix icd-10-gm: <https://biomedit.ch/rdf/sphn-resource/icd-10-gm/> .
@prefix obi: <http://purl.obolibrary.org/obo/OBI_> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix sh: <http://www.w3.org/ns/shacl#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix snomed: <http://snomed.info/id/> .
@prefix so: <http://purl.obolibrary.org/obo/SO_> .
@prefix sphn-atc: <https://biomedit.ch/rdf/sphn-resource/atc/> .
@prefix sphn-loinc: <https://biomedit.ch/rdf/sphn-resource/loinc/> .
@prefix ucum: <https://biomedit.ch/rdf/sphn-resource/ucum/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix ex: <http://example.org/> .

constraints:AccessDevice a sh:NodeShape ;
    sh:closed false ;
    sh:ignoredProperties ( rdf:type ) ;
    sh:property [ sh:maxCount 1 ;
            sh:message "constraint:AccessDevice_1",
                "message:MinCount, Or, or MaxCount constraint violated, expected minCount is 0 and maxCount is 1 and expected one of the following: https://biomedit.ch/rdf/sphn-schema/sphn#Code, http://snomed.info/id/105789008, https://biomedit.ch/rdf/sphn-schema/sphn#Terminology",
                "sparql:SELECT ?this (COUNT(?o) AS ?actualCount) ?actual WHERE { ?this <https://biomedit.ch/rdf/sphn-schema/sphn#hasTypeCode> ?o . ?o rdf:type ?actual . }",
                "template:MinCount, Or, or MaxCount constraint violated on {this} on hasTypeCode, expected minCount is 0 and maxCount is 1 and expected one of the following: https://biomedit.ch/rdf/sphn-schema/sphn#Code, http://snomed.info/id/105789008, https://biomedit.ch/rdf/sphn-schema/sphn#Terminology, found {actualCount} objects of type {actual}" ;
            sh:minCount 0 ;
            sh:or ( [ sh:class :Code ] [ sh:class snomed:105789008 ] [ sh:class :Terminology ] ) ;
            sh:path :hasTypeCode ],
        [ sh:maxCount 1 ;
            sh:message "constraint:AccessDevice_2",
                "message:MinCount, Or, or MaxCount constraint violated, expected minCount is 0 and maxCount is 1 and expected one of the following: https://biomedit.ch/rdf/sphn-schema/sphn#Code, https://biomedit.ch/rdf/sphn-schema/sphn#Terminology",
                "sparql:SELECT ?this (COUNT(?o) AS ?actualCount) ?actual WHERE { ?this <https://biomedit.ch/rdf/sphn-schema/sphn#hasProductCode> ?o . ?o rdf:type ?actual . }",
                "template:MinCount, Or, or MaxCount constraint violated on {this} on hasProductCode, expected minCount is 0 and maxCount is 1 and expected one of the following: https://biomedit.ch/rdf/sphn-schema/sphn#Code, https://biomedit.ch/rdf/sphn-schema/sphn#Terminology, found {actualCount} objects of type {actual}" ;
            sh:minCount 0 ;
            sh:or ( [ sh:class :Code ] [ sh:class :Terminology ] ) ;
            sh:path :hasProductCode ] ;
    sh:targetClass :AccessDevice .

ex:test a :AccessDevice ;
    :hasTypeCode ex:dummy ;
    :hasTypeCode ex:dummy2 .

ex:dummy a ex:dummyType1 .
ex:dummy2 a ex:dummyType2 .

Validation Report with Blank Node/s

@prefix :            <https://biomedit.ch/rdf/sphn-schema/sphn#> .
@prefix chop:        <https://biomedit.ch/rdf/sphn-resource/chop/> .
@prefix constraints: <https://biomedit.ch/rdf/sphn-schema-constraints/sphn#> .
@prefix dash:        <http://datashapes.org/dash#> .
@prefix dcterms:     <http://purl.org/dc/terms/> .
@prefix eco:         <http://purl.obolibrary.org/obo/ECO_> .
@prefix edam:        <http://edamontology.org/> .
@prefix efo:         <http://www.ebi.ac.uk/efo/EFO_> .
@prefix emdn:        <https://biomedit.ch/rdf/sphn-resource/emdn/> .
@prefix ex:          <http://example.org/> .
@prefix genepio:     <http://purl.obolibrary.org/obo/GENEPIO_> .
@prefix geno:        <http://purl.obolibrary.org/obo/GENO_> .
@prefix graphql:     <http://datashapes.org/graphql#> .
@prefix icd-10-gm:   <https://biomedit.ch/rdf/sphn-resource/icd-10-gm/> .
@prefix obi:         <http://purl.obolibrary.org/obo/OBI_> .
@prefix owl:         <http://www.w3.org/2002/07/owl#> .
@prefix rdf:         <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs:        <http://www.w3.org/2000/01/rdf-schema#> .
@prefix sh:          <http://www.w3.org/ns/shacl#> .
@prefix skos:        <http://www.w3.org/2004/02/skos/core#> .
@prefix snomed:      <http://snomed.info/id/> .
@prefix so:          <http://purl.obolibrary.org/obo/SO_> .
@prefix sphn-atc:    <https://biomedit.ch/rdf/sphn-resource/atc/> .
@prefix sphn-loinc:  <https://biomedit.ch/rdf/sphn-resource/loinc/> .
@prefix swa:         <http://topbraid.org/swa#> .
@prefix tosh:        <http://topbraid.org/tosh#> .
@prefix ucum:        <https://biomedit.ch/rdf/sphn-resource/ucum/> .
@prefix xsd:         <http://www.w3.org/2001/XMLSchema#> .

_:b0    sh:maxCount  1 ;
        sh:message   "template:MinCount, Or, or MaxCount constraint violated on {this} on hasTypeCode, expected minCount is 0 and maxCount is 1 and expected one of the following: https://biomedit.ch/rdf/sphn-schema/sphn#Code, http://snomed.info/id/105789008, https://biomedit.ch/rdf/sphn-schema/sphn#Terminology, found {actualCount} objects of type {actual}" , "sparql:SELECT ?this (COUNT(?o) AS ?actualCount) ?actual WHERE { ?this <https://biomedit.ch/rdf/sphn-schema/sphn#hasTypeCode> ?o . ?o rdf:type ?actual . }" , "message:MinCount, Or, or MaxCount constraint violated, expected minCount is 0 and maxCount is 1 and expected one of the following: https://biomedit.ch/rdf/sphn-schema/sphn#Code, http://snomed.info/id/105789008, https://biomedit.ch/rdf/sphn-schema/sphn#Terminology" , "constraint:AccessDevice_1" ;
        sh:minCount  0 ;
        sh:or        ( [ sh:class  :Code ]
                       [ sh:class  snomed:105789008 ]
                       [ sh:class  :Terminology ]
                     ) ;
        sh:path      :hasTypeCode .

[ rdf:type     sh:ValidationReport ;
  sh:conforms  false ;
  sh:result    [ rdf:type                      sh:ValidationResult ;
                 sh:focusNode                  ex:test ;
                 sh:resultMessage              "constraint:AccessDevice_1" , "sparql:SELECT ?this (COUNT(?o) AS ?actualCount) ?actual WHERE { ?this <https://biomedit.ch/rdf/sphn-schema/sphn#hasTypeCode> ?o . ?o rdf:type ?actual . }" , "message:MinCount, Or, or MaxCount constraint violated, expected minCount is 0 and maxCount is 1 and expected one of the following: https://biomedit.ch/rdf/sphn-schema/sphn#Code, http://snomed.info/id/105789008, https://biomedit.ch/rdf/sphn-schema/sphn#Terminology" , "template:MinCount, Or, or MaxCount constraint violated on {this} on hasTypeCode, expected minCount is 0 and maxCount is 1 and expected one of the following: https://biomedit.ch/rdf/sphn-schema/sphn#Code, http://snomed.info/id/105789008, https://biomedit.ch/rdf/sphn-schema/sphn#Terminology, found {actualCount} objects of type {actual}" ;
                 sh:resultPath                 :hasTypeCode ;
                 sh:resultSeverity             sh:Violation ;
                 sh:sourceConstraintComponent  sh:MaxCountConstraintComponent ;
                 sh:sourceShape                _:b0
               ] ;
  sh:result    [ rdf:type                      sh:ValidationResult ;
                 sh:focusNode                  ex:test ;
                 sh:resultMessage              "sparql:SELECT ?this (COUNT(?o) AS ?actualCount) ?actual WHERE { ?this <https://biomedit.ch/rdf/sphn-schema/sphn#hasTypeCode> ?o . ?o rdf:type ?actual . }" , "constraint:AccessDevice_1" , "template:MinCount, Or, or MaxCount constraint violated on {this} on hasTypeCode, expected minCount is 0 and maxCount is 1 and expected one of the following: https://biomedit.ch/rdf/sphn-schema/sphn#Code, http://snomed.info/id/105789008, https://biomedit.ch/rdf/sphn-schema/sphn#Terminology, found {actualCount} objects of type {actual}" , "message:MinCount, Or, or MaxCount constraint violated, expected minCount is 0 and maxCount is 1 and expected one of the following: https://biomedit.ch/rdf/sphn-schema/sphn#Code, http://snomed.info/id/105789008, https://biomedit.ch/rdf/sphn-schema/sphn#Terminology" ;
                 sh:resultPath                 :hasTypeCode ;
                 sh:resultSeverity             sh:Violation ;
                 sh:sourceConstraintComponent  sh:OrConstraintComponent ;
                 sh:sourceShape                _:b0 ;
                 sh:value                      ex:dummy
               ] ;
  sh:result    [ rdf:type                      sh:ValidationResult ;
                 sh:focusNode                  ex:test ;
                 sh:resultMessage              "template:MinCount, Or, or MaxCount constraint violated on {this} on hasTypeCode, expected minCount is 0 and maxCount is 1 and expected one of the following: https://biomedit.ch/rdf/sphn-schema/sphn#Code, http://snomed.info/id/105789008, https://biomedit.ch/rdf/sphn-schema/sphn#Terminology, found {actualCount} objects of type {actual}" , "message:MinCount, Or, or MaxCount constraint violated, expected minCount is 0 and maxCount is 1 and expected one of the following: https://biomedit.ch/rdf/sphn-schema/sphn#Code, http://snomed.info/id/105789008, https://biomedit.ch/rdf/sphn-schema/sphn#Terminology" , "constraint:AccessDevice_1" , "sparql:SELECT ?this (COUNT(?o) AS ?actualCount) ?actual WHERE { ?this <https://biomedit.ch/rdf/sphn-schema/sphn#hasTypeCode> ?o . ?o rdf:type ?actual . }" ;
                 sh:resultPath                 :hasTypeCode ;
                 sh:resultSeverity             sh:Violation ;
                 sh:sourceConstraintComponent  sh:OrConstraintComponent ;
                 sh:sourceShape                _:b0 ;
                 sh:value                      ex:dummy2
               ]
] .
ensaremirerol commented 10 months ago

I've refactored code based on your feedback. Thanks!