Test more things in each query using shacl

glyconnect/1.ttl

@@ -1,12 +1,14 @@
 prefix ex: <https://glyconnect.expasy.org/.well-known/sparql-examples> 
 prefix up: <http://purl.uniprot.org/core/> 
 prefix sh: <http://www.w3.org/ns/shacl#> 
+prefix schema: <https://schema.org/>
 prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> 
 
 ex:1
     a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ;
     sh:prefixes ex: ;
+    schema:target <https://glyconnect.expasy.org/sparql> ;
     rdfs:comment """Get all Glyconnect proteins their Uniprot reference isoform""" ;
     sh:select """SELECT distinct ?glycoprotein ?isoform
 where {

glyconnect/2.ttl

@@ -2,11 +2,13 @@ prefix ex: <https://glyconnect.expasy.org/.well-known/sparql-examples>
 prefix up: <http://purl.uniprot.org/core/> 
 prefix sh: <http://www.w3.org/ns/shacl#> 
 prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+prefix schema: <https://schema.org/>
 prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> 
 
 ex:2
     a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ;
     sh:prefixes ex: ;
+    schema:target <https://glyconnect.expasy.org/sparql> ;
     rdfs:comment """Get all Glyconnect glycan with their graphical SNFG representation""" ;
     sh:select """SELECT distinct ?structure ?image 
 where {

glyconnect/3.ttl

@@ -2,11 +2,13 @@ prefix ex: <https://glyconnect.expasy.org/sparql>
 prefix up: <http://purl.uniprot.org/core/> 
 prefix sh: <http://www.w3.org/ns/shacl#> 
 prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+prefix schema: <https://schema.org/>
 prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> 
 
 ex:3
     a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ;
     sh:prefixes ex: ;
+    schema:target <https://glyconnect.expasy.org/sparql> ;
     rdfs:comment """Select all glycosylations (glycan, protein, position) with their reference articles""" ;
     sh:select """SELECT distinct ?glycoprotein ?isoform ?position ?structure ?image  ?citation ?pmid
 where {

glyconnect/4.ttl

@@ -2,11 +2,13 @@ prefix ex: <https://glyconnect.expasy.org/.well-known/sparql-examples>
 prefix up: <http://purl.uniprot.org/core/> 
 prefix sh: <http://www.w3.org/ns/shacl#> 
 prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+prefix schema: <https://schema.org/>
 prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> 
 
 ex:4
     a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ;
     sh:prefixes ex: ;
+    schema:target <https://glyconnect.expasy.org/sparql> ;
     rdfs:comment """Select all glycosylations (glycan, protein, position) with their associated disease where the name start with 'cancer'""" ;
     sh:select """SELECT distinct ?glycoprotein ?isoform ?position ?structure ?disease ?diseasename
 where {

glyconnect/5.ttl

@@ -3,9 +3,11 @@ prefix up: <http://purl.uniprot.org/core/>
 prefix sh: <http://www.w3.org/ns/shacl#> 
 prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> 
+prefix schema: <https://schema.org/>
 
 ex:5
     a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ;
+    schema:target <https://glyconnect.expasy.org/sparql> ;
     sh:prefixes ex: ;
     rdfs:comment """Get all Glyconnect reference papers""" ;
     sh:select """SELECT distinct ?citation ?pmid

metanetx/1.ttl

@@ -2,9 +2,12 @@ prefix ex: <https://sparql.metanetx.org/.well-known/sparql-examples/>
 prefix sh: <http://www.w3.org/ns/shacl#> 
 prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> 
+prefix schema: <https://schema.org/>
+
 ex:1
     a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ;
     sh:prefixes ex: ;
+    schema:target <https://rdf.metanetx.org/sparql/> ;
     rdfs:comment """Retrieve the MNXref metabolite with name *N,N-dimethyl-beta-alanine*, together with molecular information.""" ;
     sh:select """SELECT ?metabolite ?label ?source ?formula ?charge ?inchi ?inchikey ?smiles
 WHERE {

pom.xml

@@ -37,6 +37,13 @@
 				<type>pom</type>
 				<scope>import</scope>
 			</dependency>
+			<dependency>
+				<groupId>org.eclipse.rdf4j</groupId>
+				<artifactId>rdf4j-bom</artifactId>
+				<version>${rdf4j.version}</version>
+				<type>pom</type>
+				<scope>import</scope>
+			</dependency>
 		</dependencies>
 	</dependencyManagement>
 	<dependencies>
@@ -54,43 +61,46 @@
 		<dependency>
 			<groupId>org.eclipse.rdf4j</groupId>
 			<artifactId>rdf4j-rio-turtle</artifactId>
-			<version>${rdf4j.version}</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.eclipse.rdf4j</groupId>
 			<artifactId>rdf4j-model</artifactId>
-			<version>${rdf4j.version}</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.eclipse.rdf4j</groupId>
 			<artifactId>rdf4j-model-api</artifactId>
-			<version>${rdf4j.version}</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.eclipse.rdf4j</groupId>
 			<artifactId>rdf4j-model-vocabulary</artifactId>
-			<version>${rdf4j.version}</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.eclipse.rdf4j</groupId>
 			<artifactId>rdf4j-sail-model</artifactId>
-			<version>${rdf4j.version}</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.eclipse.rdf4j</groupId>
 			<artifactId>rdf4j-sail-memory</artifactId>
-			<version>${rdf4j.version}</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.rdf4j</groupId>
+			<artifactId>rdf4j-repository-api</artifactId>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.eclipse.rdf4j</groupId>
 			<artifactId>rdf4j-repository-sail</artifactId>
-			<version>${rdf4j.version}</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.rdf4j</groupId>
+			<artifactId>rdf4j-shacl</artifactId>
 			<scope>test</scope>
 		</dependency>
 	</dependencies>

src/test/java/swiss/sib/rdf/sparql/examples/CreateTestWithRDF4jMethods.java

@@ -5,28 +5,58 @@
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.junit.jupiter.api.Assertions.fail;
 
+import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
+import java.io.StringReader;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.util.Iterator;
 import java.util.stream.Stream;
 
+import org.eclipse.rdf4j.common.exception.ValidationException;
+import org.eclipse.rdf4j.model.IRI;
 import org.eclipse.rdf4j.model.Model;
+import org.eclipse.rdf4j.model.Statement;
 import org.eclipse.rdf4j.model.Value;
 import org.eclipse.rdf4j.model.impl.LinkedHashModel;
 import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
+import org.eclipse.rdf4j.model.vocabulary.RDF4J;
 import org.eclipse.rdf4j.model.vocabulary.SHACL;
 import org.eclipse.rdf4j.query.MalformedQueryException;
 import org.eclipse.rdf4j.query.parser.QueryParser;
 import org.eclipse.rdf4j.query.parser.sparql.SPARQLParserFactory;
+import org.eclipse.rdf4j.repository.Repository;
+import org.eclipse.rdf4j.repository.RepositoryConnection;
+import org.eclipse.rdf4j.repository.RepositoryException;
+import org.eclipse.rdf4j.repository.sail.SailRepository;
 import org.eclipse.rdf4j.rio.RDFFormat;
 import org.eclipse.rdf4j.rio.RDFHandlerException;
 import org.eclipse.rdf4j.rio.RDFParseException;
 import org.eclipse.rdf4j.rio.RDFParser;
 import org.eclipse.rdf4j.rio.Rio;
 import org.eclipse.rdf4j.rio.helpers.StatementCollector;
+import org.eclipse.rdf4j.rio.turtle.TurtleWriter;
+import org.eclipse.rdf4j.sail.memory.MemoryStore;
+import org.eclipse.rdf4j.sail.shacl.ShaclSail;
 
 public class CreateTestWithRDF4jMethods {
+	private static final String shaclOneIdOneQuery = """
+			PREFIX sh:<http://www.w3.org/ns/shacl#>
+			PREFIX schema:<https://schema.org/>
+
+			[] sh:targetClass sh:SPARQLExecutable ;
+				sh:property [
+					sh:path [ sh:alternativePath ( sh:select sh:ask sh:describe sh:construct ) ] ;
+					sh:maxCount 1 ;
+					sh:minCount 1
+				] , [
+					sh:path rdfs:comment ;
+					sh:maxCount 1 ;
+					sh:minCount 1 ] , [
+				sh:path schema:target;
+					sh:minCount 1 ].
+			""";
 
 	static void testQueryValid(Path p, String projectPrefixes) {
 		assertTrue(Files.exists(p));
@@ -40,9 +70,8 @@ static void testQueryValid(Path p, String projectPrefixes) {
 		}
 		assertFalse(model.isEmpty());
 		QueryParser parser = new SPARQLParserFactory().getParser();
-		Stream.of("ask", "select", "concat", "describe")
-				.map(s -> model.getStatements(null,
-						SimpleValueFactory.getInstance().createIRI(SHACL.NAMESPACE, s), null))
+		Stream.of("ask", "select", "concat", "describe").map(
+				s -> model.getStatements(null, SimpleValueFactory.getInstance().createIRI(SHACL.NAMESPACE, s), null))
 				.map(Iterable::iterator).forEach(i -> {
 					while (i.hasNext()) {
 						Value obj = i.next().getObject();
@@ -60,4 +89,67 @@ static void testQueryValid(Path p, String projectPrefixes) {
 
 	}
 
+	/**
+	 * Use shacl to test all the turtle files contain an rdfs:comment and one query.
+	 * Also makes a test that all example IRIs are unique.
+	 * 
+	 * @param paths
+	 */
+	static void testShaclContsraints(Stream<Path> paths) {
+		MemoryStore memoryStore = new MemoryStore();
+		try {
+			memoryStore.init();
+
+			ShaclSail shaclSail = new ShaclSail(memoryStore);
+			Repository repo = new SailRepository(shaclSail);
+			try (RepositoryConnection connection = repo.getConnection();
+					StringReader sr = new StringReader(shaclOneIdOneQuery)) {
+				// add shapes
+				connection.begin();
+				connection.add(sr, RDFFormat.TURTLE, RDF4J.SHACL_SHAPE_GRAPH);
+				connection.commit();
+			} catch (RDFParseException | RepositoryException | IOException e) {
+				fail(e);
+			}
+			try (RepositoryConnection connection = repo.getConnection()) {
+				paths.forEach(p -> testValidatingAFile(connection, p));
+			}
+			repo.shutDown();
+			shaclSail.shutDown();
+		} finally {
+			memoryStore.shutDown();
+		}
+	}
+
+	private static void testValidatingAFile(RepositoryConnection connection, Path p) {
+		assertTrue(Files.exists(p));
+		connection.begin();
+		try {
+			IRI iri = connection.getValueFactory().createIRI(p.toUri().toString());
+			connection.add(p.toFile(), iri);
+			connection.commit();
+		} catch (RDFParseException | RepositoryException | IOException e) {
+			if (e.getCause() instanceof ValidationException ve) {
+				String report = validationReportAsString(ve);
+				fail(p.toUri() + " failed " + ve + '\n'+ report, e.getCause());
+			}
+			fail(e);
+		}
+		assertFalse(connection.size() == 0);
+	}
+
+	private static String validationReportAsString(ValidationException ve) {
+		Model vem = ve.validationReportAsModel();
+		var boas = new ByteArrayOutputStream();
+		TurtleWriter tw = new TurtleWriter(boas);
+		tw.startRDF();
+		Iterator<Statement> iterator = vem.iterator();
+		while(iterator.hasNext()) {
+			tw.handleStatement(iterator.next());
+		}
+		tw.endRDF();
+		String report = boas.toString();
+		return report;
+	}
+
 }

src/test/java/swiss/sib/rdf/sparql/examples/ValidateSparqlExamplesTest.java

@@ -22,6 +22,7 @@
 import org.apache.jena.riot.RDFDataMgr;
 import org.apache.jena.riot.RiotException;
 import org.junit.jupiter.api.DynamicTest;
+import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.TestFactory;
 import org.junit.jupiter.api.function.Executable;
 
@@ -51,11 +52,21 @@ public Stream<DynamicTest> testAllWithRDF4j() throws URISyntaxException, IOExcep
 		return testAll(tester);
 	}
 
+	@Test
+	public void testUniqueIdentifierPerQueries() throws URISyntaxException, IOException {
+		CreateTestWithRDF4jMethods.testShaclContsraints(Files.walk(getBasePath(), 5).filter(this::isTurtleButNotPrefixFile));
+	}
+
 	@TestFactory
 	public Stream<DynamicTest> testPrefixDeclarations() throws URISyntaxException, IOException {
+		Path basePath = getBasePath();
+		return Files.walk(basePath, 5).filter(this::isTurtleAndPrefixFile).flatMap(this::testPrefixes);
+	}
+
+	private Path getBasePath() throws URISyntaxException {
 		URL baseDir = getClass().getResource("/");
 		Path basePath = Paths.get(baseDir.toURI());
-		return Files.walk(basePath, 5).filter(this::isTurtleAndPrefixFile).flatMap(this::testPrefixes);
+		return basePath;
 	}
 
 	private Stream<DynamicTest> testAll(BiFunction<Path, String, Executable> tester)

uniprot/10.ttl

@@ -5,7 +5,6 @@ prefix schema:<https://schema.org/>
 prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 
 prefix faldo:<http://biohackathon.org/resource/faldo#>
 prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#>
-prefix schema:<http://schema.org/>
 ex:10
     a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ;
     sh:prefixes _:sparql_examples_prefixes ;

uniprot/11.ttl

@@ -5,7 +5,6 @@ prefix schema:<https://schema.org/>
 prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 
 prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#>
 prefix faldo:<http://biohackathon.org/resource/faldo#> 
-prefix schema:<http://schema.org/>
 ex:11
     a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ;
     sh:prefixes _:sparql_examples_prefixes ;

uniprot/15.ttl

@@ -6,6 +6,7 @@ prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#>
 ex:15
     a sh:SPARQLExecutable, sh:SPARQLExecutable ;
+    schema:target <https://sparql.uniprot.org/sparql/> ;
     rdfs:comment """Select all triples that relate to the EMBL CDS entry AA089367.1: """;
     sh:describe """DESCRIBE <http://purl.uniprot.org/embl-cds/AAO89367.1>
 """ .

uniprot/21.ttl

@@ -5,7 +5,6 @@ prefix schema:<https://schema.org/>
 prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 
 prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#>
 prefix skos:<http://www.w3.org/2004/02/skos/core#> 
-prefix schema:<http://schema.org/>
 ex:21
     a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ;
     sh:prefixes _:sparql_examples_prefixes ;

uniprot/27.ttl

@@ -4,7 +4,6 @@ prefix sh: <http://www.w3.org/ns/shacl#>
 prefix schema:<https://schema.org/>
 prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 
 prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#>
-prefix schema:<http://schema.org/>
 ex:27
     a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ;
     sh:prefixes _:sparql_examples_prefixes ;

uniprot/28.ttl

@@ -4,7 +4,7 @@ prefix sh: <http://www.w3.org/ns/shacl#>
 prefix schema:<https://schema.org/>
 prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 
 prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> 
-prefix schema:<http://schema.org/>
+
 ex:28
     a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ;
     sh:prefixes _:sparql_examples_prefixes ;

uniprot/29.ttl

@@ -5,7 +5,6 @@ prefix schema:<https://schema.org/>
 prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 
 prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> 
 prefix allie: <http://allie.dbcls.jp/>
-prefix schema:<http://schema.org/>
 ex:29
     a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ;
     sh:prefixes _:sparql_examples_prefixes ;

uniprot/30.ttl

@@ -5,7 +5,6 @@ prefix schema:<https://schema.org/>
 prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 
 prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> 
 prefix taxon:<http://purl.uniprot.org/taxonomy/> 
-prefix schema:<http://schema.org/>
 ex:30
     a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ;
     sh:prefixes _:sparql_examples_prefixes ;

uniprot/31.ttl

@@ -5,7 +5,6 @@ prefix schema:<https://schema.org/>
 prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 
 prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> 
 prefix taxon:<http://purl.uniprot.org/taxonomy/> 
-prefix schema:<http://schema.org/>
 ex:31
     a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ;
     sh:prefixes _:sparql_examples_prefixes ;