fix(xmlvalidate): duplicate cardinalities of LinkValues (DEV-4203) (#…

…1198)

src/dsp_tools/commands/xml_validate/api_connection.py

@@ -50,6 +50,11 @@ def _get(self, url: str, headers: dict[str, Any] | None = None) -> Response:
             raise UserError(msg)
         return response
 
+    def get_knora_api(self) -> str:
+        url = f"{self.api_url}/ontology/knora-api/v2#"
+        onto = self._get(url, headers={"Accept": "text/turtle"})
+        return onto.text
+
     def get_ontologies(self) -> list[str]:
         """
         Returns a list of project ontologies as a string in turtle format.

src/dsp_tools/commands/xml_validate/deserialise_input.py

@@ -1,5 +1,6 @@
 from typing import Callable
 from typing import Sequence
+from typing import cast
 
 from lxml import etree
 
@@ -50,7 +51,7 @@ def _deserialise_all_resources(root: etree._Element) -> DataDeserialised:
     all_res: list[AbstractResource] = []
     for res in root.iterchildren():
         res_id = res.attrib["id"]
-        lbl = res.attrib["label"]
+        lbl = cast(str, res.attrib.get("label"))
         match res.tag:
             case "resource":
                 all_res.append(_deserialise_one_resource(res))

src/dsp_tools/commands/xml_validate/reformat_validaton_result.py

@@ -86,4 +86,4 @@ def _reformat_onto_iri(prop: str) -> str:
 
 
 def _reformat_data_iri(iri: str) -> str:
-    return iri.lstrip("http://data/")
+    return iri.replace("http://data/", "")

src/dsp_tools/commands/xml_validate/sparql/resource_shacl.py

@@ -36,7 +36,8 @@ def _construct_resource_nodeshape(onto_graph: Graph) -> Graph:
     } WHERE {
 
         ?class a owl:Class ;
-               knora-api:isResourceClass true .
+               knora-api:isResourceClass true ;
+               knora-api:canBeInstantiated true .
 
         BIND(IRI(CONCAT(str(?class), "_Shape")) AS ?shapesIRI)
     }
@@ -79,11 +80,13 @@ def _construct_1_cardinality(onto_graph: Graph) -> Graph:
     
       ?class a owl:Class ;
           knora-api:isResourceClass true ;
+          knora-api:canBeInstantiated true ;
           rdfs:subClassOf ?restriction .
       ?restriction a owl:Restriction ;
           owl:onProperty ?propRestriction ;
           salsah-gui:guiOrder ?order ;
           owl:cardinality 1 .
+      FILTER NOT EXISTS { ?propRestriction knora-api:isLinkValueProperty true }
     
       BIND(IRI(CONCAT(str(?class), "_Shape")) AS ?shapesIRI)
     }
@@ -117,11 +120,13 @@ def _construct_0_1_cardinality(onto_graph: Graph) -> Graph:
     
       ?class a owl:Class ;
           knora-api:isResourceClass true ;
+          knora-api:canBeInstantiated true ;
           rdfs:subClassOf ?restriction .
       ?restriction a owl:Restriction ;
           owl:onProperty ?propRestriction ;
           salsah-gui:guiOrder ?order ;
           owl:maxCardinality 1 .
+      FILTER NOT EXISTS { ?propRestriction knora-api:isLinkValueProperty true }
     
       BIND(IRI(CONCAT(str(?class), "_Shape")) AS ?shapesIRI)
     }
@@ -154,11 +159,13 @@ def _construct_1_n_cardinality(onto_graph: Graph) -> Graph:
     
       ?class a owl:Class ;
           knora-api:isResourceClass true ;
+          knora-api:canBeInstantiated true ;
           rdfs:subClassOf ?restriction .
       ?restriction a owl:Restriction ;
           owl:onProperty ?propRestriction ;
           salsah-gui:guiOrder ?order ;
           owl:minCardinality 1 .
+      FILTER NOT EXISTS { ?propRestriction knora-api:isLinkValueProperty true }
     
       BIND(IRI(CONCAT(str(?class), "_Shape")) AS ?shapesIRI)
     }
@@ -188,11 +195,13 @@ def _construct_0_n_cardinality(onto_graph: Graph) -> Graph:
     
       ?class a owl:Class ;
           knora-api:isResourceClass true ;
+          knora-api:canBeInstantiated true ;
           rdfs:subClassOf ?restriction .
       ?restriction a owl:Restriction ;
           owl:onProperty ?propRestriction ;
           salsah-gui:guiOrder ?order ;
           owl:minCardinality 0 .
+      FILTER NOT EXISTS { ?propRestriction knora-api:isLinkValueProperty true }
     
       BIND(IRI(CONCAT(str(?class), "_Shape")) AS ?shapesIRI)
     }

src/dsp_tools/commands/xml_validate/xml_validate.py

@@ -1,4 +1,5 @@
 import warnings
+from copy import deepcopy
 from pathlib import Path
 
 from lxml import etree
@@ -39,10 +40,11 @@ def xml_validate(filepath: Path, api_url: str, dev_route: bool) -> bool:  # noqa
     _inform_about_experimental_feature()
     data_rdf, shortcode = _get_data_info_from_file(filepath, api_url)
     onto_con = OntologyConnection(api_url, shortcode)
-    ontologies = _get_project_ontos(onto_con)
-    data_graph = data_rdf.make_graph() + ontologies
+    ontologies, shapes = _get_shacl(onto_con)
+    data_graph = data_rdf.make_graph()
+    # data_graph += ontologies
     val = ShaclValidator(api_url)
-    report = _validate(val, ontologies, data_graph)
+    report = _validate(val, shapes, data_graph)
     if report.conforms:
         cprint("\n   Validation passed!   ", color="green", attrs=["bold", "reverse"])
     else:
@@ -68,28 +70,38 @@ def _inform_about_experimental_feature() -> None:
     warnings.warn(DspToolsUserWarning(LIST_SEPARATOR.join(what_is_validated)))
 
 
-def _validate(validator: ShaclValidator, onto_graph: Graph, data_graph: Graph) -> ValidationReport:
-    shapes = construct_shapes_graph(onto_graph)
-    shape_str = shapes.serialize(format="ttl")
+def _validate(validator: ShaclValidator, shapes_graph: Graph, data_graph: Graph) -> ValidationReport:
+    shape_str = shapes_graph.serialize(format="ttl")
     data_str = data_graph.serialize(format="ttl")
     results = validator.validate(data_str, shape_str)
     conforms = bool(next(results.objects(None, SH.conforms)))
     return ValidationReport(
         conforms=conforms,
         validation_graph=results,
-        shacl_graph=shapes,
+        shacl_graph=shapes_graph,
         data_graph=data_graph,
     )
 
 
+def _get_shacl(onto_con: OntologyConnection) -> tuple[Graph, Graph]:
+    ontologies = _get_project_ontos(onto_con)
+    knora_ttl = onto_con.get_knora_api()
+    kag = Graph()
+    kag.parse(data=knora_ttl, format="ttl")
+    onto_for_construction = deepcopy(ontologies) + kag
+    shapes = construct_shapes_graph(onto_for_construction)
+    shapes += ontologies
+    return ontologies, shapes
+
+
 def _get_project_ontos(onto_con: OntologyConnection) -> Graph:
     all_ontos = onto_con.get_ontologies()
-    g = Graph()
+    onto_g = Graph()
     for onto in all_ontos:
         og = Graph()
         og.parse(data=onto, format="ttl")
-        g += og
-    return g
+        onto_g += og
+    return onto_g
 
 
 def _get_data_info_from_file(file: Path, api_url: str) -> tuple[DataRDF, str]:

test/unittests/commands/xml_validate/conftest.py

@@ -1,3 +1,4 @@
 from test.unittests.commands.xml_validate.fixtures_data_deserialised import *  # noqa: F403
 from test.unittests.commands.xml_validate.fixtures_data_rdf import *  # noqa: F403
+from test.unittests.commands.xml_validate.fixtures_onto import *  # noqa: F403
 from test.unittests.commands.xml_validate.fixtures_xml_data import *  # noqa: F403

test/unittests/commands/xml_validate/fixtures_onto.py

@@ -0,0 +1,96 @@
+import pytest
+from rdflib import Graph
+from rdflib import Namespace
+
+ONTO = Namespace("http://0.0.0.0:3333/ontology/9999/onto/v2#")
+API_SHAPES = Namespace("http://api.knora.org/ontology/knora-api/shapes/v2#")
+PREFIXES = """
+@prefix knora-api: <http://api.knora.org/ontology/knora-api/v2#> .
+@prefix onto: <http://0.0.0.0:3333/ontology/9999/onto/v2#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix salsah-gui: <http://api.knora.org/ontology/salsah-gui/v2#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+"""
+
+
+@pytest.fixture
+def link_prop_card_1() -> Graph:
+    ttl = f"""{PREFIXES}
+    onto:ClassMixedCard a owl:Class ;
+    rdfs:label "Resource with all cardinality options" ;
+    knora-api:canBeInstantiated true ;
+    knora-api:isResourceClass true ;
+    rdfs:subClassOf [ 
+            a owl:Restriction ;
+            salsah-gui:guiOrder 1 ;
+            owl:cardinality 1 ;
+            owl:onProperty onto:testHasLinkToCardOneResourceValue 
+            ] ,
+            [ a owl:Restriction ;
+            salsah-gui:guiOrder 1 ;
+            owl:cardinality 1 ;
+            owl:onProperty onto:testHasLinkToCardOneResource ] .
+            
+    onto:testHasLinkToCardOneResource a owl:ObjectProperty ;
+        rdfs:label "Super-class" ;
+        knora-api:isEditable true ;
+        knora-api:isLinkProperty true ;
+        knora-api:isResourceProperty true ;
+        knora-api:objectType onto:CardOneResource ;
+        salsah-gui:guiElement salsah-gui:Searchbox ;
+        rdfs:subPropertyOf knora-api:hasLinkTo .
+    
+    onto:testHasLinkToCardOneResourceValue a owl:ObjectProperty ;
+        rdfs:label "Super-class" ;
+        knora-api:isEditable true ;
+        knora-api:isLinkValueProperty true ;
+        knora-api:isResourceProperty true ;
+        knora-api:objectType knora-api:LinkValue ;
+        salsah-gui:guiElement salsah-gui:Searchbox ;
+        rdfs:subPropertyOf knora-api:hasLinkToValue .
+    """
+    g = Graph()
+    g.parse(data=ttl, format="ttl")
+    return g
+
+
+@pytest.fixture
+def link_prop_card_01() -> Graph:
+    ttl = f"""{PREFIXES}
+    onto:ClassMixedCard a owl:Class ;
+    rdfs:label "Resource with all cardinality options" ;
+    knora-api:canBeInstantiated true ;
+    knora-api:isResourceClass true ;
+    rdfs:subClassOf [ 
+            a owl:Restriction ;
+            salsah-gui:guiOrder 1 ;
+            owl:maxCardinality 1 ;
+            owl:onProperty onto:testHasLinkToCardOneResourceValue 
+            ] ,
+            [ a owl:Restriction ;
+            salsah-gui:guiOrder 1 ;
+            owl:maxCardinality 1 ;
+            owl:onProperty onto:testHasLinkToCardOneResource ] .
+
+    onto:testHasLinkToCardOneResource a owl:ObjectProperty ;
+        rdfs:label "Super-class" ;
+        knora-api:isEditable true ;
+        knora-api:isLinkProperty true ;
+        knora-api:isResourceProperty true ;
+        knora-api:objectType onto:CardOneResource ;
+        salsah-gui:guiElement salsah-gui:Searchbox ;
+        rdfs:subPropertyOf knora-api:hasLinkTo .
+
+    onto:testHasLinkToCardOneResourceValue a owl:ObjectProperty ;
+        rdfs:label "Super-class" ;
+        knora-api:isEditable true ;
+        knora-api:isLinkValueProperty true ;
+        knora-api:isResourceProperty true ;
+        knora-api:objectType knora-api:LinkValue ;
+        salsah-gui:guiElement salsah-gui:Searchbox ;
+        rdfs:subPropertyOf knora-api:hasLinkToValue .
+    """
+    g = Graph()
+    g.parse(data=ttl, format="ttl")
+    return g

test/unittests/commands/xml_validate/test_sparql_resource_shacl.py

@@ -86,6 +86,7 @@ def card_1() -> Graph:
     ttl = f"""{PREFIXES}
     onto:ClassMixedCard a owl:Class ;
         knora-api:isResourceClass true ;
+        knora-api:canBeInstantiated true ;
         rdfs:subClassOf [ 
                 a owl:Restriction ;
                 salsah-gui:guiOrder 0 ;
@@ -103,6 +104,7 @@ def card_0_1() -> Graph:
     ttl = f"""{PREFIXES}
     onto:ClassMixedCard a owl:Class ;
         knora-api:isResourceClass true ;
+        knora-api:canBeInstantiated true ;
         rdfs:subClassOf [ 
                 a owl:Restriction ;
                 salsah-gui:guiOrder 1 ;
@@ -120,6 +122,7 @@ def card_1_n() -> Graph:
     ttl = f"""{PREFIXES}
     onto:ClassMixedCard a owl:Class ;
         knora-api:isResourceClass true ;
+        knora-api:canBeInstantiated true ;
         rdfs:subClassOf [ 
                 a owl:Restriction ;
                 salsah-gui:guiOrder 2 ;
@@ -137,6 +140,7 @@ def card_0_n() -> Graph:
     ttl = f"""{PREFIXES}
     onto:ClassMixedCard a owl:Class ;
         knora-api:isResourceClass true ;
+        knora-api:canBeInstantiated true ;
         rdfs:subClassOf [ 
                 a owl:Restriction ;
                 salsah-gui:guiOrder 3 ;
@@ -172,7 +176,7 @@ def test_cardinality_0_1(self, onto_graph: Graph) -> None:
 
     def test_cardinality_0_n(self, onto_graph: Graph) -> None:
         result = _construct_0_n_cardinality(onto_graph)
-        number_of_occurrences_in_onto = 24
+        number_of_occurrences_in_onto = 21  # Inheritance included
         triples_card_0_n = 3 * number_of_occurrences_in_onto
         assert len(result) == triples_card_0_n
 
@@ -231,6 +235,18 @@ def test_good(self, card_1: Graph) -> None:
         assert next(result.objects(bn, SH.severity)) == SH.Violation
         assert str(next(result.objects(bn, SH.message))) == "1"
 
+    def test_good_link_value(self, link_prop_card_1: Graph) -> None:
+        result = _construct_1_cardinality(link_prop_card_1)
+        assert len(result) == 7
+        bn = next(result.subjects(RDF.type, SH.PropertyShape))
+        shape_iri = next(result.subjects(SH.property, bn))
+        assert shape_iri == ONTO.ClassMixedCard_Shape
+        assert str(next(result.objects(bn, SH.minCount))) == "1"
+        assert str(next(result.objects(bn, SH.maxCount))) == "1"
+        assert next(result.objects(bn, SH.path)) == ONTO.testHasLinkToCardOneResource
+        assert next(result.objects(bn, SH.severity)) == SH.Violation
+        assert str(next(result.objects(bn, SH.message))) == "1"
+
     def test_empty_0_1(self, card_0_1: Graph) -> None:
         result = _construct_1_cardinality(card_0_1)
         assert len(result) == 0
@@ -257,6 +273,18 @@ def test_good(self, card_0_1: Graph) -> None:
         assert next(result.objects(bn, SH.severity)) == SH.Violation
         assert str(next(result.objects(bn, SH.message))) == "0-1"
 
+    def test_good_link_value(self, link_prop_card_01: Graph) -> None:
+        result = _construct_0_1_cardinality(link_prop_card_01)
+        assert len(result) == 7
+        bn = next(result.subjects(RDF.type, SH.PropertyShape))
+        shape_iri = next(result.subjects(SH.property, bn))
+        assert shape_iri == ONTO.ClassMixedCard_Shape
+        assert str(next(result.objects(bn, SH.minCount))) == "0"
+        assert str(next(result.objects(bn, SH.maxCount))) == "1"
+        assert next(result.objects(bn, SH.path)) == ONTO.testHasLinkToCardOneResource
+        assert next(result.objects(bn, SH.severity)) == SH.Violation
+        assert str(next(result.objects(bn, SH.message))) == "0-1"
+
     def test_empty_1(self, card_1: Graph) -> None:
         result = _construct_0_1_cardinality(card_1)
         assert len(result) == 0

testdata/xml-validate/data/cardinality_correct.xml

@@ -23,13 +23,19 @@
         </boolean-prop>
     </resource>
 
-    <resource label="Card Mixed" restype=":ClassMixedCard" id="id_3">
+    <resource label="Card 1" restype=":ClassInheritedCardinality" id="id_3">
+        <text-prop name=":testSimpleText">
+            <text encoding="utf8">Text</text>
+        </text-prop>
+    </resource>
+
+    <resource label="Card Mixed" restype=":ClassMixedCard" id="id_4">
         <boolean-prop name=":testBoolean">
             <boolean>true</boolean>
         </boolean-prop>
-        <decimal-prop name=":testDecimalSimpleText">
-            <decimal>2.71</decimal>
-        </decimal-prop>
+        <resptr-prop name=":testHasLinkToCardOneResource">
+            <resptr>id_2</resptr>
+        </resptr-prop>
         <geoname-prop name=":testGeoname">
             <geoname>1111111</geoname>
             <geoname>2222222</geoname>

testdata/xml-validate/data/cardinality_violation.xml

@@ -23,20 +23,20 @@
         <boolean-prop name=":testBoolean">
             <boolean>true</boolean>
         </boolean-prop>
-        <decimal-prop name=":testDecimalSimpleText">
-            <decimal>2.71</decimal>
-            <decimal>2.00</decimal>
-        </decimal-prop>
+        <resptr-prop name=":testHasLinkToCardOneResource">
+            <resptr>id_closed_constraint</resptr>
+            <resptr>id_card_one</resptr>
+        </resptr-prop>
         <geoname-prop name=":testGeoname">
             <geoname>111111</geoname>
         </geoname-prop>
     </resource>
 
     <!-- 'testGeoname' cardinality 1-n -->
     <resource label="Geoname Card 1-n" restype=":ClassMixedCard" id="id_min_card">
-        <boolean-prop name=":testBoolean">
-            <boolean>true</boolean>
-        </boolean-prop>
+        <resptr-prop name=":testHasLinkToCardOneResource">
+            <resptr>id_closed_constraint</resptr>
+        </resptr-prop>
     </resource>
 
 </knora>