Commit e66bcb65 authored by Maxime Lefrançois's avatar Maxime Lefrançois
Browse files

grouped warnings and errors

parent 692b12f9

src/main/java/fr/emse/gitlab/saref/jobs/ReadOntology.java

+51 −20
Original line number Diff line number Diff line
@@ -7,10 +7,13 @@ import java.io.InputStreamReader; 
import java.nio.charset.Charset;

import java.nio.charset.MalformedInputException;

import java.text.SimpleDateFormat;

import java.util.ArrayList;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.stream.Collectors;



import org.apache.jena.atlas.RuntimeIOException;

import org.apache.jena.datatypes.xsd.XSDDatatype;
@@ -58,7 +61,8 @@ public class ReadOntology extends JobRunner { 
			+ "    ?violation sh:focusNode ?focusNode .\n" + "    ?violation sh:resultMessage ?resultMessage .\n"

			+ "    ?violation sh:resultSeverity ?severity .\n"

			+ "      OPTIONAL { ?violation sh:resultPath ?resultPath . }\n"

			+ "      OPTIONAL { ?violation sh:value ?value . } \n" + "}";

			+ "      OPTIONAL { ?violation sh:value ?value . } \n" + "}"

			+ "ORDER BY ?severity ?resultMessage ?focusNode ";



	static final Map<String, String> PREFIXES = new HashMap<String, String>();

	static {
@@ -95,7 +99,8 @@ public class ReadOntology extends JobRunner { 
			model.read(input, Constants.BASE, Lang.TTL.getLabel());

		} catch (Exception ex) {

			if (ex instanceof RuntimeIOException && ex.getCause() instanceof MalformedInputException) {

				try (InputStreamReader  input2 = new InputStreamReader(new FileInputStream(ontologyFile), Charset.defaultCharset())) {

				try (InputStreamReader input2 = new InputStreamReader(new FileInputStream(ontologyFile),

						Charset.defaultCharset())) {

					model.read(input2, Constants.BASE, Lang.TTL.getLabel());

				} catch (Exception ex2) {

					logger.error("Exception while reading the ontology file", ex2);
@@ -157,20 +162,46 @@ public class ReadOntology extends JobRunner { 
			reportModel.setNsPrefixes(PREFIXES);

			reportModel.setNsPrefix("sh", "http://www.w3.org/ns/shacl#");

			try (QueryExecution exec = QueryExecutionFactory.create(SELECT_VIOLATION, reportModel);) {

				Resource previousSeverity = null;

				Literal previousResultMessage = null;

				List<Resource> previousFocusNodes = new ArrayList<>();

				List<RDFNode> previousvalues = new ArrayList<>();

				for (ResultSet resultSet = exec.execSelect(); resultSet.hasNext();) {

					QuerySolution sol = resultSet.next();

					Resource severity = sol.getResource("severity");

					Resource focusNode = sol.get("focusNode").asResource();

					Literal resultMessage = sol.getLiteral("resultMessage");

					Resource focusNode = sol.get("focusNode").asResource();

					RDFNode value = sol.get("value");

					String gotString = (value != null && value.isURIResource()) ? String.format(" Got: %s", value)

							: "";

					if (severity != null && severity.getURI().equals(SHACL_VIOLATION)) {

						logger.error(String.format("Shape violation on node %s: %s%s", focusNode, resultMessage,

								gotString));



					if (severity != null && severity.equals(previousSeverity) && resultMessage != null

							&& resultMessage.equals(previousResultMessage)) {

						previousFocusNodes.add(focusNode);

						previousvalues.add(value);

					} else {

						if (previousSeverity != null) {

							String message = String.format("%s: %s", previousResultMessage,

									String.join(" - ", previousFocusNodes.stream().map(Object::toString)

											.collect(Collectors.toList()).toArray(new String[1])));

							if (severity.getURI().equals(SHACL_VIOLATION)) {

								logger.error(message);

							} else {

								logger.warn(message);

							}

						}

						previousSeverity = severity;

						previousResultMessage = resultMessage;

						previousFocusNodes = new ArrayList<>();

						previousvalues = new ArrayList<>();

					}

				}

				if (!previousFocusNodes.isEmpty()) {

					String message = String.format("%s: %s", previousResultMessage,

							String.join(" - ", previousFocusNodes.stream().map(Object::toString)

									.collect(Collectors.toList()).toArray(new String[1])));

					if (previousSeverity != null && previousSeverity.getURI().equals(SHACL_VIOLATION)) {

						logger.error(message);

					} else {

						logger.warn(String.format("Shape violation on node %s: %s%s", focusNode, resultMessage,

								gotString));

						logger.warn(message);

					}

				}

			}
@@ -281,6 +312,7 @@ public class ReadOntology extends JobRunner { 
		model.add(DCTerms.license, RDF.type, OWL.AnnotationProperty);

		model.add(SCHEMA.Person, RDF.type, OWL.Class);

		model.add(SCHEMA.Organization, RDF.type, OWL.Class);

		model.add(SCHEMA.affiliation, RDF.type, OWL.ObjectProperty);

		model.add(SCHEMA.familyName, RDF.type, OWL.DatatypeProperty);

		model.add(SCHEMA.givenName, RDF.type, OWL.DatatypeProperty);

		model.add(SCHEMA.name, RDF.type, OWL.DatatypeProperty);
@@ -304,14 +336,14 @@ public class ReadOntology extends JobRunner { 
		model.removeAll(ontologySeries, VANN.preferredNamespacePrefix, null);

		model.removeAll(ontologySeries, VANN.preferredNamespaceUri, null);

		model.add(ontologySeries, VANN.preferredNamespacePrefix, version.getRepository().getPrefix());

		model.add(ontologySeries, VANN.preferredNamespaceUri, version.getRepository().getNamespace(), XSDDatatype.XSDanyURI);

		model.add(ontologySeries, VANN.preferredNamespaceUri, version.getRepository().getNamespace(),

				XSDDatatype.XSDanyURI);



		model.removeAll(ontologySeries, DCTerms.issued, null);

		model.add(ontologySeries, DCTerms.issued, SIMPLE_DATE_FORMAT.format(version.getIssued()), XSDDatatype.XSDdate);

	}



	private void computeTerms(Version version, Model model, Set<Resource> definedTerms,

			Set<Resource> usedTerms) {

	private void computeTerms(Version version, Model model, Set<Resource> definedTerms, Set<Resource> usedTerms) {

		model.listStatements().forEachRemaining(stmt -> {

			Resource s = stmt.getSubject();

			Resource p = stmt.getPredicate();
@@ -322,8 +354,7 @@ public class ReadOntology extends JobRunner { 
		});

	}



	private void computeTerms(Version version, Resource t, Set<Resource> definedTerms,

			Set<Resource> usedTerms) {

	private void computeTerms(Version version, Resource t, Set<Resource> definedTerms, Set<Resource> usedTerms) {

		if (t == null || !t.isURIResource() || !t.getURI().startsWith(Constants.BASE) || t.getURI().endsWith("/")) {

			return;

		}

src/main/resources/sarefShape.ttl

+45 −118
Original line number Diff line number Diff line
@@ -22,19 +22,19 @@ sarefsh:OntologyShape 
		sh:path owl:versionInfo ;

		sh:maxCount 0 ;

		sh:severity sh:Warning ;

		sh:message "The annotation owl:versionInfo shall not be set in the source file, as it will be computed automatically."

		sh:message "The annotation owl:versionInfo should not be set in the source file, as it will be computed automatically"

	] ;

	sh:property [

		sh:path owl:versionIRI ;

		sh:maxCount 0 ;

		sh:severity sh:Warning ;

		sh:message "The annotation owl:versionIRI shall not be set in the source file, as it will be computed automatically."

		sh:message "The annotation owl:versionIRI should not be set in the source file, as it will be computed automatically"

	] ;

	sh:property [

		sh:path owl:priorVersion ;

		sh:maxCount 0 ;

		sh:severity sh:Warning ;

		sh:message "The annotation owl:priorVersion shall not be set in the source file, as it will be computed automatically."

		sh:message "The annotation owl:priorVersion should not be set in the source file, as it will be computed automatically"

	] ;

	sh:property [

		sh:path owl:imports ;
@@ -49,7 +49,7 @@ sarefsh:OntologyShape 
		sh:minCount 1 ;

		sh:maxCount 1 ;

		sh:severity sh:Violation ;

		sh:message "The ontology should have exactly one <http://purl.org/dc/terms/title>."

		sh:message "The ontology shall have exactly one <http://purl.org/dc/terms/title>"

	] ;  

	sh:property [

		sh:path dcterms:abstract ;
@@ -57,7 +57,7 @@ sarefsh:OntologyShape 
		sh:minCount 1 ;

		sh:maxCount 1 ;

		sh:severity sh:Warning ;

		sh:message "The ontology should have exactly one <http://purl.org/dc/terms/abstract>."

		sh:message "The ontology should have exactly one <http://purl.org/dc/terms/abstract>"

	] ;

	sh:property [

		sh:path dcterms:description ;
@@ -65,7 +65,7 @@ sarefsh:OntologyShape 
		sh:minCount 1 ;

		sh:maxCount 1 ;

		sh:severity sh:Warning ;

		sh:message "The ontology should have exactly one <http://purl.org/dc/terms/description>."

		sh:message "The ontology should have exactly one <http://purl.org/dc/terms/description>"

	] ;

	sh:property [

		sh:path rdfs:comment ;
@@ -83,7 +83,7 @@ sarefsh:OntologyShape 
		sh:datatype xsd:date ;

		sh:maxCount 0 ;

		sh:severity sh:Warning ;

		sh:message "The annotation <http://purl.org/dc/terms/modified> shall not be set in the source file, as it will be computed automatically."

		sh:message "The annotation <http://purl.org/dc/terms/modified> will be computed automatically"

	] ;

	sh:property [

		sh:path dcterms:source ;
@@ -96,51 +96,51 @@ sarefsh:OntologyShape 
		sh:minCount 1 ;

		sh:pattern "https://forge.etsi.org/etsi-software-license" ;

		sh:severity sh:Violation ;

		sh:message "There shall be at least one annotation <http://purl.org/dc/terms/license> <https://forge.etsi.org/etsi-software-license>."

		sh:message "There shall be at least one annotation <http://purl.org/dc/terms/license> <https://forge.etsi.org/etsi-software-license>"

	] ;

  sh:property [

    sh:path dcterms:creator ;

    sh:nodeKind sh:BlankNodeOrIRI ;

    sh:minCount 0 ;

    sh:severity sh:Warning ;

    sh:message "The <http://purl.org/dc/terms/creator> shall be blank nodes or IRIs."

    sh:message "The <http://purl.org/dc/terms/creator> should be blank nodes or IRIs"

  ] ;

  sh:property [

    sh:path dcterms:creator ;

    sh:severity sh:Warning ;

    sh:node sarefsh:PersonShape ;

    sh:message "Every creator shall be a <http://schema.org/Person> with <http://schema.org/givenName>, <http://schema.org/familyName>, and <http://schema.org/affiliation>."

    sh:message "Every creator should be a <http://schema.org/Person> with <http://schema.org/givenName>, <http://schema.org/familyName>, and <http://schema.org/affiliation>"

  ] ;

	sh:property [

		sh:path dcterms:contributor ;

		sh:nodeKind sh:BlankNodeOrIRI ;

		sh:minCount 0 ;

		sh:severity sh:Warning ;

		sh:message "The <http://purl.org/dc/terms/contributor> shall be blank nodes or IRIs."

		sh:message "The <http://purl.org/dc/terms/contributor> should be blank nodes or IRIs"

	] ;

	sh:property [

		sh:path dcterms:contributor ;

		sh:severity sh:Warning ;

		sh:node sarefsh:PersonShape ;

		sh:message "Every contributor shall be a <http://schema.org/Person> with <http://schema.org/givenName>, <http://schema.org/familyName>, and <http://schema.org/affiliation>."

		sh:message "Every contributor should be a <http://schema.org/Person> with <http://schema.org/givenName>, <http://schema.org/familyName>, and <http://schema.org/affiliation>"

	] ;

	sh:property [

		sh:path dcterms:publisher ;

		sh:maxCount 0 ;

		sh:severity sh:Warning ;

		sh:message "The annotation <http://purl.org/dc/terms/publisher> shall not be set in the source file, as it will be computed automatically."

		sh:message "The annotation <http://purl.org/dc/terms/publisher> will be computed automatically"

	] ;

	sh:property [

		sh:path vann:preferredNamespacePrefix ;

		sh:maxCount 0 ;

		sh:severity sh:Warning ;

		sh:message "The annotation <http://purl.org/vocab/vann/preferredNamespacePrefix> shall not be set in the source file, as it will be computed automatically."

		sh:message "The annotation <http://purl.org/vocab/vann/preferredNamespacePrefix> will be computed automatically"

	] ;

	sh:property [

		sh:path vann:preferredNamespaceUri ;

		sh:maxCount 0 ;

		sh:severity sh:Warning ;

		sh:message "The annotation <http://purl.org/vocab/vann/preferredNamespaceUri> shall not be set in the source file, as it will be computed automatically."

		sh:message "The annotation <http://purl.org/vocab/vann/preferredNamespaceUri> will be computed automatically"

	] .

	

sarefsh:PersonShape
@@ -151,19 +151,19 @@ sarefsh:PersonShape 
    sh:path rdf:type ;

    sh:hasValue schema:Person ;

		sh:severity sh:Warning ;

    sh:message "Each contributor shall be a <http://schema.org/Person>."

    sh:message "Every contributor should be a <http://schema.org/Person>"

	] ;

	sh:property [

    sh:path schema:givenName ;

    sh:minCount 1 ;

		sh:severity sh:Warning ;

    sh:message "Each contributor shall have at least one <http://schema.org/givenName>."

    sh:message "Every contributor should have at least one <http://schema.org/givenName>"

	] ;

	sh:property [

    sh:path schema:familyName ;

    sh:minCount 1 ;

		sh:severity sh:Warning ;

    sh:message "Each contributor shall have at least one <http://schema.org/lastName>."

    sh:message "Every contributor should have at least one <http://schema.org/lastName>"

	] ;

	sh:property [

    sh:path schema:affiliation ;
@@ -171,7 +171,7 @@ sarefsh:PersonShape 
		sh:nodeKind sh:BlankNodeOrIRI ;

		sh:node sarefsh:AffiliationShape ;

		sh:severity sh:Warning ;

    sh:message "Each contributor shall have at least one <http://schema.org/affiliation>, that shall be a blank node or a IRI of type <http://schema.org/Organization> with at least one <http://schema.org/name>."

    sh:message "Every contributor should have at least one <http://schema.org/affiliation>, that should be a blank node or a IRI of type <http://schema.org/Organization> with at least one <http://schema.org/name>"

	] .

	

sarefsh:AffiliationShape
@@ -182,112 +182,39 @@ sarefsh:AffiliationShape 
    sh:path rdf:type ;

    sh:hasValue schema:Organization ;

		sh:severity sh:Warning ;

    sh:message "The affiliation of each contributor shall be a <http://schema.org/Organization>."

    sh:message "The affiliation of each contributor should be a <http://schema.org/Organization>"

	] ;

	sh:property [

    sh:path schema:name ;

    sh:minCount 1 ;

		sh:severity sh:Warning ;

    sh:message "The affiliation of each contributor shall have at least one <http://schema.org/name>."

    sh:message "The affiliation of each contributor should have at least one <http://schema.org/name>"

	] .	



[] a sh:NodeShape ;

  sh:targetClass owl:Class ;

  sh:message "The owl:Class should have at least one rdfs:label and one rdfs:comment" ;

  sh:targetClass owl:Class,  owl:ObjectProperty, owl:DatatypeProperty , owl:NamedIndividual;

  sh:message "The following terms do not have at least one rdfs:label" ;

  sh:severity sh:Warning ;

  sh:or (

    [ sh:nodeKind sh:BlankNode ]

  	[

  	  sh:and (

    [ 

      sh:path rdfs:label ;

      sh:nodeKind sh:Literal ;

      sh:minCount 1 ;

      sh:severity sh:Warning ;

					sh:message "The term should have at least one rdfs:label."

				] 

			  [

					sh:path rdfs:comment ;

					sh:nodeKind sh:Literal ;

					sh:minCount 1 ;

					sh:severity sh:Warning ;

					sh:message "The term should have at least one rdfs:comment."

				] 

	  	)

      sh:message "The term should have at least one rdfs:label"

    ]

  ) .

[] a sh:NodeShape ;

  sh:targetClass owl:ObjectProperty ;

  sh:message "The owl:ObjectProperty should have at least one rdfs:label and one rdfs:comment" ;

  sh:targetClass owl:Class,  owl:ObjectProperty, owl:DatatypeProperty , owl:NamedIndividual;

  sh:message "The following terms do not have at least one rdfs:comment" ;

  sh:severity sh:Warning ;

  sh:or (

    [ sh:nodeKind sh:BlankNode ]

  	[

  	  sh:and (

  	  	[ 

  	  	  sh:path rdfs:label ;

					sh:nodeKind sh:Literal ;

					sh:minCount 1 ;

					sh:severity sh:Warning ;

					sh:message "The term should have at least one rdfs:label."

				] 

    [ 

      sh:path rdfs:comment ;

      sh:nodeKind sh:Literal ;

      sh:minCount 1 ;

      sh:severity sh:Warning ;

					sh:message "The term should have at least one rdfs:comment."

				] 

	  	)

		] 

	) .

[] a sh:NodeShape ;

  sh:targetClass owl:DatatypeProperty ;

  sh:message "The owl:DatatypeProperty should have at least one rdfs:label and one rdfs:comment" ;

	sh:severity sh:Warning ;

  sh:or (

  	[ sh:nodeKind sh:BlankNode ]

  	[

  	  sh:and (

  	  	[ 

  	  	  sh:path rdfs:label ;

					sh:nodeKind sh:Literal ;

					sh:minCount 1 ;

					sh:severity sh:Warning ;

					sh:message "The term should have at least one rdfs:label."

				] 

			  [

					sh:path rdfs:comment ;

					sh:nodeKind sh:Literal ;

					sh:minCount 1 ;

					sh:severity sh:Warning ;

					sh:message "The term should have at least one rdfs:comment."

				] 

	  	)

		] 

	) .

[] a sh:NodeShape ;

  sh:targetClass owl:NamedIndividual ;

  sh:message "The owl:NamedIndividual should have at least one rdfs:label and one rdfs:comment" ;

	sh:severity sh:Warning ;

  sh:or (

  	[ sh:nodeKind sh:BlankNode ]

  	[

  	  sh:and (

  	  	[ 

  	  	  sh:path rdfs:label ;

					sh:nodeKind sh:Literal ;

					sh:minCount 1 ;

					sh:severity sh:Warning ;

					sh:message "The term should have at least one rdfs:label."

				] 

			  [

					sh:path rdfs:comment ;

					sh:nodeKind sh:Literal ;

					sh:minCount 1 ;

					sh:severity sh:Warning ;

					sh:message "The term should have at least one rdfs:comment."

				] 

	  	)

      sh:message "The term should have at least one rdfs:comment"

    ]

  ) .