First version of shacl validation of live handle record

Author: Ziroli Plutschow

src/integration-test/java/org/nanopub/TheseTestsRequireOtherSystemsIT.java

@@ -5,6 +5,7 @@
 import org.eclipse.rdf4j.rio.RDFFormat;
 import org.eclipse.rdf4j.rio.RDFWriter;
 import org.eclipse.rdf4j.rio.Rio;
+import org.junit.Assert;
 import org.junit.jupiter.api.Test;
 import org.nanopub.extra.security.SignNanopub;
 import org.nanopub.extra.security.SignatureAlgorithm;
@@ -80,11 +81,19 @@ void retrieveMetadataFromHandleSystem() throws URISyntaxException, IOException,
         // it would be great to compare all statements here
     }
 
-//     @Test // TODO
-    void validateFdo () throws URISyntaxException, IOException, InterruptedException, MalformedNanopubException {
-        String id = "21.T11967/39b0ec87d17a4856c5f7";
+    @Test
+    void validateValidFdo() throws URISyntaxException, IOException, InterruptedException, MalformedNanopubException {
+        String id = "21.T11966/82045bd97a0acce88378";
         FdoMetadata metadata = RetrieveFdo.retrieveMetadataFromId(id);
-        ValidateFdo.isValid(metadata);
+
+        Assert.assertTrue(ValidateFdo.isValid(metadata));
     }
 
+    @Test
+    void validateInvalidFdo() throws URISyntaxException, IOException, InterruptedException, MalformedNanopubException {
+        String id = "21.T11967/39b0ec87d17a4856c5f7";
+        FdoMetadata metadata = RetrieveFdo.retrieveMetadataFromId(id);
+
+        Assert.assertFalse(ValidateFdo.isValid(metadata));
+    }
 }

src/main/java/org/nanopub/fdo/FdoMetadata.java

@@ -89,7 +89,7 @@ public String getSchemaUrl() {
 		Value schemaEntry = tuples.get(vf.createIRI(FDO_TYPE_PREFIX + "21.T11966/JsonSchema"));
 		if (schemaEntry != null) {
 			// assume the entry looks like {"$ref": "https://the-url"}
-			String url = schemaEntry.stringValue().substring(10, schemaEntry.stringValue().length() - 3);
+			String url = schemaEntry.stringValue().substring(10, schemaEntry.stringValue().length() - 2);
 			return url;
 		}
 		return null;

src/main/java/org/nanopub/fdo/ShaclValidator.java

@@ -47,12 +47,26 @@ public static void main(String[] args) {
         }
     }
 
+
+    private static void printStatements(Set<Statement> statements) {
+        for (Statement s : statements) {
+            System.out.println(s.getSubject().toString() + " " + s.getPredicate().toString() + " " + s.getObject().toString());
+        }
+    }
+
     /**
      * Logs constraints validation to System.out
      *
      * @return true, iff the data respects the specification of the shape.
      */
     public static boolean validateShacl(Set<Statement> shape, Set<Statement> data) {
+
+//        // Debug info
+//        System.out.println("Validating Data ");
+//        printStatements(data);
+//        System.out.println("Against Schema ");
+//        printStatements(shape);
+
         ShaclSail shaclSail = new ShaclSail(new MemoryStore());
         Repository repo = new SailRepository(shaclSail);
 

src/main/java/org/nanopub/fdo/ValidateFdo.java

@@ -1,14 +1,42 @@
 package org.nanopub.fdo;
 
+import com.google.gson.Gson;
+import org.eclipse.rdf4j.model.IRI;
+import org.eclipse.rdf4j.model.Statement;
+import org.eclipse.rdf4j.model.ValueFactory;
+import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
+import org.eclipse.rdf4j.model.vocabulary.RDF;
 import org.nanopub.MalformedNanopubException;
+import org.nanopub.fdo.rest.gson.ParsedSchemaResponse;
 
 import java.io.IOException;
+import java.net.URI;
 import java.net.URISyntaxException;
+import java.net.http.HttpClient;
+import java.net.http.HttpRequest;
+import java.net.http.HttpResponse;
+import java.util.HashSet;
+import java.util.Set;
+
+import static org.nanopub.fdo.FdoNanopubCreator.FDO_TYPE_PREFIX;
 
 // TODO class that provides the Op.Validate operations.
 //      See https://fdo-connect.gitlab.io/ap1/architecture-documentation/main/operation-specification/
 public class ValidateFdo {
 
+	private static final ValueFactory vf = SimpleValueFactory.getInstance();
+
+	private static final IRI SHACL_MAX_COUNT = vf.createIRI("http://www.w3.org/ns/shacl#maxCount");
+	private static final IRI SHACL_MIN_COUNT = vf.createIRI("http://www.w3.org/ns/shacl#minCount");
+	private static final IRI SHACL_PATH = vf.createIRI("http://www.w3.org/ns/shacl#path");
+	private static final IRI SHACL_TARGET = vf.createIRI("http://www.w3.org/ns/shacl#targetClass");
+	private static final IRI SHACL_PROPERTY = vf.createIRI("http://www.w3.org/ns/shacl#property");
+	private static final IRI SHACL_NODE_SHAPE = vf.createIRI("http://www.w3.org/ns/shacl#NodeShape");
+
+	private static final IRI TEMP_TYPE = vf.createIRI("https://w3id.org/kpxl/temptype");
+
+	private static HttpClient client = HttpClient.newHttpClient();
+
 	private ValidateFdo() {}  // no instances allowed
 
 	// TODO Just a boolean as return value. Later probably an object that also includes errors/warnings.
@@ -17,11 +45,42 @@ public static boolean isValid(FdoMetadata fdoMetadata) throws MalformedNanopubEx
 		String profileId = FdoUtils.extractHandle(fdoMetadata.getProfile());
 		String schemaUrl = RetrieveFdo.retrieveMetadataFromHandle(profileId).getSchemaUrl();
 
-		// TODO get construct shacl from schema
-		throw new RuntimeException("Not yet implemented");
+		HttpRequest req = HttpRequest.newBuilder().GET().uri(new URI(schemaUrl)).build();
+		HttpResponse<String> httpResponse = client.send(req, HttpResponse.BodyHandlers.ofString());
+
+		Set<Statement> shaclShape = createShaclShapeFromJson(httpResponse);
+		Set<Statement> data = addTypeStatement(fdoMetadata);
 
-		// return ShaclValidator.validateShacl(shaclShape, fdoMetadata.getStatements());
+		System.out.println("Validating FdoMetadata " + fdoMetadata.getId());
+		System.out.println("Against Schema " + schemaUrl);
+
+		return ShaclValidator.validateShacl(shaclShape, data);
+	}
+
+	private static Set<Statement> addTypeStatement(FdoMetadata fdoMetadata) {
+		Set<Statement> data = fdoMetadata.getStatements();
+		Statement first = data.toArray(new Statement[0])[0];
+		data.add(vf.createStatement(first.getSubject(), RDF.TYPE, TEMP_TYPE));
+		return data;
 	}
 
+	public static Set<Statement> createShaclShapeFromJson(HttpResponse<String> httpResponse) {
+		ParsedSchemaResponse r = new Gson().fromJson(httpResponse.body(), ParsedSchemaResponse.class);
+
+		Set<Statement> shaclShape = new HashSet<>();
+		String SUBJ_PREFIX = "https://w3id.org/kpxl/shacl/temp/";
+		int i = 0;
+		for (String s: r.required) {
+			i++;
+			shaclShape.add(vf.createStatement(vf.createIRI(SUBJ_PREFIX+i), SHACL_MAX_COUNT, vf.createLiteral(1)));
+			shaclShape.add(vf.createStatement(vf.createIRI(SUBJ_PREFIX+i), SHACL_MIN_COUNT, vf.createLiteral(1)));
+			shaclShape.add(vf.createStatement(vf.createIRI(SUBJ_PREFIX+i), SHACL_PATH, vf.createIRI(FDO_TYPE_PREFIX + s)));
+			shaclShape.add(vf.createStatement(vf.createIRI(SUBJ_PREFIX), SHACL_PROPERTY, vf.createIRI(SUBJ_PREFIX+i)));
+		}
+		shaclShape.add(vf.createStatement(FdoUtils.createIri(SUBJ_PREFIX), SHACL_TARGET, TEMP_TYPE));
+		shaclShape.add(vf.createStatement(FdoUtils.createIri(SUBJ_PREFIX), RDF.TYPE, SHACL_NODE_SHAPE));
+
+		return shaclShape;
+	}
 
 }

src/main/java/org/nanopub/fdo/rest/gson/ParsedSchemaResponse.java

@@ -0,0 +1,5 @@
+package org.nanopub.fdo.rest.gson;
+
+public class ParsedSchemaResponse {
+    public String[] required;
+}