Merge pull request #331 from geneontology/add-cardinality-to-shex-val…

…idation-report

Add cardinality to shex validation report

minerva-core/src/main/java/org/geneontology/minerva/validation/ShexConstraint.java

@@ -7,6 +7,8 @@
 
 import com.google.gson.annotations.SerializedName;
 
+import fr.inria.lille.shexjava.util.Interval;
+
 /**
  * @author bgood
  *
@@ -16,12 +18,30 @@ public class ShexConstraint {
 	String property;
 	Set<String> node_types;
 	Set<String> object_types;
+	String cardinality;
+	int nobjects;
 
 	@SerializedName("matched_range_shapes")
 	Set<String> matched_range_shapes;
 
 
 
+	public String getCardinality() {
+		return cardinality;
+	}
+
+	public void setCardinality(String cardinality) {
+		this.cardinality = cardinality;
+	}
+
+	public int getNobjects() {
+		return nobjects;
+	}
+
+	public void setNobjects(int nobjects) {
+		this.nobjects = nobjects;
+	}
+
 	public Set<String> getMatched_range_shapes() {
 		return matched_range_shapes;
 	}
@@ -64,6 +84,13 @@ public ShexConstraint(String object, String property, Set<String> intended_range
 		this.object_types = object_types;
 	}
 
+	public ShexConstraint(String property, String cardinality, int nobjects) {
+		super();
+		this.property = property;
+		this.cardinality = cardinality;
+		this.nobjects = nobjects;
+	}
+
 	public Set<String> getIntended_range_shapes() {
 		return intended_range_shapes;
 	}

minerva-core/src/test/java/org/geneontology/minerva/validation/ShexValidatorTest.java

@@ -77,20 +77,26 @@ public void testShexMetadata() throws IOException {
 		validate("src/test/resources/validation/should_pass/", shexMeta, should_be_valid);	
 	}
 
+	@Test 
+	public void testTmp() throws IOException {
+		boolean should_be_valid = false;
+		validate("src/test/resources/validation/tmp/", shex, should_be_valid);	
+	}
+
 	public void validate(String dir, ShexValidator shex, boolean should_be_valid) throws IOException {
 		File directory = new File(dir);
 		if(directory.isDirectory()) {
 			for(File file : directory.listFiles()) {
 				if(file.getName().endsWith("ttl")) {
 					Model test_model = ModelFactory.createDefaultModel();
-					System.out.println("validating "+file.getAbsolutePath());
 					test_model.read(file.getAbsolutePath());
+					System.out.println("validating "+file.getAbsolutePath()+" size "+test_model.size());
 					//Note that in the live system, Arachne is executed on the model prior to this step, potentially adding inferred classes that are missed with this.
 					//this is faster and useful for debugging the shex though.  See org.geneontology.minerva.server.validation.ValidationTest in the Test branch of Minerva server for a more complete test
 					test_model = shex.enrichSuperClasses(test_model);
 					ShexValidationReport report = shex.runShapeMapValidation(test_model);
 					if(should_be_valid) {
-						assertTrue(file+" not conformant", report.isConformant());
+						assertTrue(file+" not conformant "+report.getAsText()+"\n"+report.getAsTab(""), report.isConformant());
 					}else {
 						assertFalse(file+" is conformant (should not be)", report.isConformant());
 					}

minerva-core/src/test/resources/validation/go-cam-shapes.shex

@@ -4,6 +4,7 @@ PREFIX rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX owl: <http://www.w3.org/2002/07/owl#>
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
 #metadata
 PREFIX bl: <https://w3id.org/biolink/vocab/>
 PREFIX contributor: <http://purl.org/dc/elements/1.1/contributor>
@@ -75,6 +76,7 @@ PREFIX transports_or_maintains_localization_of: <http://purl.obolibrary.org/obo/
 PREFIX directly_provides_input_for: <http://purl.obolibrary.org/obo/RO_0002413>
 PREFIX directly_positively_regulates: <http://purl.obolibrary.org/obo/RO_0002629>
 PREFIX located_in: <http://purl.obolibrary.org/obo/RO_0001025>
+PREFIX location_of: <http://purl.obolibrary.org/obo/RO_0001015>
 PREFIX happens_during: <http://purl.obolibrary.org/obo/RO_0002092>
 PREFIX regulates: <http://purl.obolibrary.org/obo/RO_0002211>
 PREFIX negatively_regulates: <http://purl.obolibrary.org/obo/RO_0002212>
@@ -122,6 +124,7 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
   date: xsd:string *; #TODO can we make this an xsd:date?
   provided_by: xsd:string *; #TODO would be better as an IRI
   rdfs:comment xsd:string *;
+  skos:note xsd:string *;
 }
 
 <GoCamEntity> IRI @<ProvenanceAnnotated> AND EXTRA a {
@@ -339,7 +342,7 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
   a ( @<MolecularFunctionClass> OR @<NegatedMolecularFunctionClass> ) {1};
   enabled_by:  ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex> ) {0,1};
   part_of: @<BiologicalProcess> {0,1};
-  occurs_in: ( @<AnatomicalEntity> OR @<ProteinContainingComplex> ) {0,1};
+  occurs_in: @<AnatomicalEntity> {0,1};
   has_output: ( @<ChemicalEntity> OR @<ProteinContainingComplex> ) *;
   has_input: ( @<ChemicalEntity> OR @<ProteinContainingComplex> ) *;
   directly_provides_input_for: @<MolecularFunction> *;
@@ -358,6 +361,10 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
   happens_during: ( @<BiologicalPhase> OR @<LifeCycleStage> OR @<PlantStructureDevelopmentStage> ) *;
 } // rdfs:comment  "A molecular function"
 
+<IdealMolecularActivity> @<MolecularFunction> AND {
+  enabled_by:  ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex> ) {1};
+}
+
 <TransporterActivityClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
   rdfs:subClassOf [ GoTransporterActivity: ];
 }
@@ -407,6 +414,7 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
 <AnatomicalEntity> @<GoCamEntity> AND EXTRA a {
   a ( @<AnatomicalEntityClass> OR @<NegatedAnatomicalEntityClass> );
   part_of: @<AnatomicalEntity> {0,1};
+  location_of: ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex> ) {0,1};
 } // rdfs:comment  "an anatomical entity"
 
 <NativeCellClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
@@ -432,12 +440,11 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
   part_of: @<AnatomicalEntity> {0,1};
   adjacent_to: @<AnatomicalEntity> *;
   overlaps: @<AnatomicalEntity> *;
-  has_part:(@<InformationBiomacromolecule> OR  @<ProteinContainingComplex>) {0,1};
 } // rdfs:comment  "a cellular component"
 
 <ProteinContainingComplex> EXTRA a {
   a @<ProteinContainingComplexClass>;
-  located_in: @<CellularComponent> {0,1};
+  located_in: @<AnatomicalEntity> {0,1};
   has_part: @<InformationBiomacromolecule> *;
 } // rdfs:comment  "a protein complex"
 
@@ -458,7 +465,8 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
 }
 <Protein> @<ChemicalEntity> AND EXTRA a {
   a @<ProteinClass> ;
-  located_in: @<CellularComponent> {0,1};
+  located_in: @<AnatomicalEntity> {0,1};
+  part_of: @<ProteinContainingComplex> {0,1};
 }// rdfs:comment  "a protein"
 
 
@@ -467,15 +475,15 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
 }
 <InformationBiomacromolecule> @<ChemicalEntity> AND EXTRA a {
    a @<InformationBiomacromoleculeClass> +;
-   part_of: @<CellularComponent> {0,1};
+   located_in: @<AnatomicalEntity> {0,1};
    part_of: @<ProteinContainingComplex> {0,1};
 }// rdfs:comment  "an information biomacromolecule - e.g. a protein or RNA product"
 
 <EvidenceClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
   rdfs:subClassOf [ GoEvidence: ] ;
 }
 
-<Evidence> @<ProvenanceAnnotated> AND EXTRA a  {
+<Evidence> @<GoCamEntity> AND EXTRA a  {
   a @<EvidenceClass> {1};
   source: xsd:string {1};
   with: xsd:string {0,1}