Add SHACL validation capabilities (#102)

connectionUtils/pom.xml

@@ -103,6 +103,13 @@
 			<artifactId>jena-arq</artifactId>
 			<version>4.9.0</version>
 		</dependency>
+
+		<!-- License: Apache 2.0 -->
+		<dependency>
+		    <groupId>org.apache.jena</groupId>
+		    <artifactId>jena-rdfconnection</artifactId>
+		    <version>4.9.0</version>
+		</dependency>
 
 		<!-- License: Apache 2.0 -->
 		<dependency>

connectionUtils/src/main/java/com/ge/research/semtk/sparqlX/SparqlConnection.java

@@ -1,5 +1,5 @@
 /**
- ** Copyright 2016-2018 General Electric Company
+ ** Copyright 2016-2023 General Electric Company
  **
  **
  ** Licensed under the Apache License, Version 2.0 (the "License");
@@ -21,6 +21,9 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 
+import org.apache.jena.graph.Graph;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdfconnection.RDFConnection;
 import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
 import org.json.simple.parser.JSONParser;
@@ -598,4 +601,35 @@ public String getUniqueKey() {
 		ret.append(this.enableOwlImports ? "owlImports;" : "noImports;");
 		return ret.toString();
 	}
+
+
+	/**
+	 * Create a Jena Graph from this SparqlConnection
+	 */
+	public Graph getJenaGraph() {
+		ArrayList<String> fetched = new ArrayList<String>();
+
+		Model model = null;
+		RDFConnection rdfConn = null;
+		try {
+			for(SparqlEndpointInterface sei : this.getAllInterfaces()) {
+				rdfConn = RDFConnection.connect(sei.getServerAndPort());
+				String graphName = sei.getGraph();
+				if(fetched.contains(sei.getServerAndPort() + graphName)) {
+					continue;  // skip if already fetched it (e.g. if model graph is the same as data graph)
+				}
+				Model m = rdfConn.fetch(graphName);
+				fetched.add(sei.getServerAndPort() + graphName);
+				if(model == null) {
+					model = m;
+				}else {
+					model.add(m);
+				}
+				rdfConn.close();
+			}
+			return model.getGraph();
+		}finally {
+			rdfConn.close();
+		}
+	}
 }

connectionUtils/src/main/java/com/ge/research/semtk/utility/Utility.java

@@ -82,6 +82,12 @@
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.text.StrSubstitutor;
+import org.apache.jena.graph.Graph;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.riot.Lang;
+import org.apache.jena.riot.RDFDataMgr;
+import org.apache.jena.riot.RDFParser;
 import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
 import org.json.simple.parser.JSONParser;
@@ -347,6 +353,17 @@ public static boolean arraysSameMinusOrder(String[] arr1, String[] arr2) {
 	    return Arrays.equals(arr1Clone, arr2Clone);
 	}
 
+	/**
+	 * Determine if two JSONObjects are equivalent.
+	 * Ignores key order (but not JSONArray list order)
+	 */
+	public static boolean equals(JSONObject o1, JSONObject o2) throws Exception {
+		ObjectMapper mapper = new ObjectMapper();
+		JsonNode json1 = mapper.readTree(o1.toString());
+		JsonNode json2 = mapper.readTree(o2.toString());
+		return json1.equals(json2);
+	}
+
 	public static String readFile(String path) throws IOException {
 		  return FileUtils.readFileToString(new File(path));
 	}
@@ -1190,5 +1207,36 @@ public FileVisitResult visitFile(Path file, BasicFileAttributes attrs)
             }
         });
     }
+
+	/**
+	 * Create a Jena Graph from Turtle data
+	 * @param ttlInputStream Turtle data in an input stream
+	 * @return the Jena graph
+	 * @throws Exception
+	 */
+	public static Graph getJenaGraphFromTurtle(InputStream ttlInputStream) throws Exception {
+		try {
+			return RDFParser.source(ttlInputStream).lang(Lang.TTL).toGraph();
+		}catch(Exception e) {
+			throw new Exception("Error creating graph from Turtle: " + e.getMessage(), e);
+		}
+	}
 
+	/**
+	 * Get a Turtle string for a given Jena Graph
+	 * @param graph the graph
+	 * @return the Turtle string
+	 */
+	public static String getTurtleFromJenaGraph(Graph graph) throws IOException {
+		OutputStream outputStream = null;
+		try {
+			Model model = ModelFactory.createModelForGraph(graph);
+			outputStream = new ByteArrayOutputStream();
+			RDFDataMgr.write(outputStream, model, Lang.TTL);
+		}finally {
+			outputStream.close();
+		}
+		return outputStream.toString();
+	}
+
 }

sparqlGraphLibrary/pom.xml

@@ -105,6 +105,13 @@
 			<artifactId>jena-arq</artifactId>
 			<version>4.9.0</version>
 		</dependency>
+
+		<!-- License: Apache 2.0 -->
+		<dependency>
+		    <groupId>org.apache.jena</groupId>
+		    <artifactId>jena-shacl</artifactId>
+		    <version>4.9.0</version>
+		</dependency>
 
 		<!-- License: Apache 2.0 -->
 		<dependency>

sparqlGraphLibrary/src/main/java/com/ge/research/semtk/belmont/ValueConstraint.java

@@ -25,8 +25,6 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import org.apache.jena.sparql.lang.SPARQLParserFactory;
-
 import com.ge.research.semtk.sparqlX.SparqlEndpointInterface;
 import com.ge.research.semtk.sparqlX.XSDSupportedType;
 import com.ge.research.semtk.utility.Utility;

sparqlGraphLibrary/src/main/java/com/ge/research/semtk/ontologyTools/PredicateStats.java

@@ -3,7 +3,6 @@
 import java.util.HashSet;
 import java.util.Hashtable;
 
-import org.apache.jena.atlas.json.JSON;
 import org.json.simple.JSONObject;
 import org.json.simple.parser.JSONParser;
 

sparqlGraphLibrary/src/main/java/com/ge/research/semtk/plotting/PlotlyPlotSpec.java

@@ -22,7 +22,6 @@
 import java.util.stream.Collectors;
 
 import org.apache.commons.lang.math.NumberUtils;
-import org.apache.jena.atlas.json.JSON;
 import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
 import org.json.simple.parser.JSONParser;

sparqlGraphLibrary/src/main/java/com/ge/research/semtk/services/client/UtilityClient.java

@@ -21,7 +21,11 @@
 import java.io.InputStreamReader;
 import java.net.ConnectException;
 
+import org.apache.jena.shacl.validation.Severity;
+
 import com.ge.research.semtk.connutil.EndpointNotFoundException;
+import com.ge.research.semtk.resultSet.SimpleResultSet;
+import com.ge.research.semtk.sparqlX.SparqlConnection;
 
 /**
  * Client for UtilityService
@@ -39,6 +43,7 @@ private void cleanUp() {
 		conf.setServiceEndpoint(null);
 		this.parametersJSON.clear();
 		this.fileParameter = null;
+		this.fileParameterName = "file";
 	}
 
 	/**
@@ -76,4 +81,37 @@ public BufferedReader execLoadIngestionPackage(File ingestionPackageFile, String
 		}
 	}
 
+
+	/**
+	 * Executes a call to run SHACL
+	 * @param shaclTtlFile		the SHACL file (in ttl format)
+	 * @param conn 				the connection
+	 * @param severity			return problems with this severity level or higher (Info, Warning, Violation)
+	 * @return 					jobId
+	 * @throws 					Exception
+	 */
+	@SuppressWarnings("unchecked")
+	public String execGetShaclResults(File shaclTtlFile, SparqlConnection conn, Severity severity) throws Exception {
+
+		if(!shaclTtlFile.exists()) {
+			throw new Exception("File does not exist: " + shaclTtlFile.getAbsolutePath());
+		}
+
+		this.parametersJSON.clear();
+		this.fileParameter = shaclTtlFile;
+		this.fileParameterName = "shaclTtlFile";
+		this.parametersJSON.put("conn", conn.toJson().toJSONString());
+		this.parametersJSON.put("severity", severity.level().getLocalName()); // e.g. Info, Warning, Violation
+		conf.setServiceEndpoint("utility/getShaclResults");
+		this.conf.setMethod(RestClientConfig.Methods.POST);
+
+		try {
+			SimpleResultSet res = this.executeWithSimpleResultReturn();
+			res.throwExceptionIfUnsuccessful();
+			return res.getJobId();
+		} finally {
+			this.cleanUp();
+		}
+	}
+
 }