src/main/java/fr/mines_stetienne/ci/saref/checkers/Clause_9_4_6_Checker.java

@@ -27,8 +27,8 @@ package fr.mines_stetienne.ci.saref.checkers;
 
 import java.io.File;
 import java.io.IOException;
-import java.util.HashMap;
-import java.util.Map;
+import java.util.ArrayList;
+import java.util.List;
 import java.net.http.HttpResponse;
 import java.nio.file.Files;
 import java.util.stream.Collectors;
@@ -74,8 +74,10 @@ public class Clause_9_4_6_Checker extends AbstractClauseChecker {
 
 		// First get the available directories. If none, not a problem.
 		File dir2 = new File(repository.getDirectory(), "patterns");
-		String[] directoryList = new String[]{};
+		List<String> shaclFileList = new ArrayList();
+		// process every shapes.ttl file in the sub-directories of the patterns directory.
 		try {
+			String[] directoryList = new String[]{};
 			String directories = Files.walk(dir2.toPath()).filter(p -> {
 				try {
 					return p.toFile().isDirectory() && !Files.isSameFile(dir2.toPath(), p);
@@ -87,24 +89,22 @@ public class Clause_9_4_6_Checker extends AbstractClauseChecker {
 				return; // no SHACL directories found.
 			}
 			directoryList = directories.split(",");
+			for(int i = 0; i < directoryList.length; i++) {
+				shaclFileList.add(directoryList[i] + "/shapes.ttl");
+			}
 		} catch (IOException e) {
 			logError(getMessage(Clause_9_4_6_Checker.MESSAGE.ioexception), e);
 		}
 
 		ShaclValidationManager.PingValidationServer();
 
-		Map<String, HttpResponse<String>> responseMap = new HashMap<String, HttpResponse<String>>();
-		// process every shapes.ttl file in the sub-directories of the patterns directory.
-		for(int i = 0; i < directoryList.length; i++) {
-			String shaclFileName = directoryList[i] + "/shapes.ttl";  // "file://" +
-			try {
-				HttpResponse<String> response = new ShaclValidationManager(ontologyToValidate).validateOntologyWithShacl(shaclFileName);
-				System.out.println(response); //<<<
-				responseMap.put(shaclFileName, response);	//<<< parse map for errors
-			} catch (IOException | InterruptedException e) {
-				logError(getMessage(Clause_9_4_6_Checker.MESSAGE.ioexception, shaclFileName));
-			}
+		//Map<String, HttpResponse<String>> responseMap = new HashMap<String, HttpResponse<String>>();
+		try {
+			ShaclValidationManager shaclValidationManager = new ShaclValidationManager(ontologyToValidate);
+			HttpResponse<String> response = shaclValidationManager.ValidateOntologyWithShacl(shaclFileList);
+			//responseMap.put(shaclFileName, response);	// parse map for errors
+		} catch (IOException | InterruptedException e) {
+			logError(getMessage(Clause_9_4_6_Checker.MESSAGE.ioexception, ontologyToValidate));
 		}
-		//System.out.println(responseMap); //<<<
 	}
 }
\ No newline at end of file

src/main/java/fr/mines_stetienne/ci/saref/managers/ShaclValidationManager.java

@@ -32,30 +32,34 @@ import java.net.URL;
 import java.net.URLEncoder;
 import java.net.http.*;
 import java.nio.file.Files;
-import java.nio.file.Path;
 import java.nio.charset.StandardCharsets;
-import java.util.HashMap;
+import java.nio.file.Paths;
 import java.util.Map;
-import java.util.Base64;
-
+import java.util.List;
+import java.util.ArrayList;
+//import java.util.HashMap;
+import org.apache.commons.lang3.StringEscapeUtils;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import fr.mines_stetienne.ci.saref.SAREFPipelineException;
 
-/*	docker run -d --name SAREFvalidator -p 8080:8080 isaitb/shacl-validator	 # runs the generic validator.
+/*	docker run -d --name SAREFvalidator -p 8080:8080 isaitb/shacl-validator	 # runs the generic validator with Dockerfile
 	Docs for RDF validator: https://www.itb.ec.europa.eu/docs/guides/latest/validatingRDF/index.html
 	Base docker image: https://hub.docker.com/r/isaitb/shacl-validator  (generic validator)
 	Use Swagger UI for testing: http://localhost:8080/shacl/swagger-ui/index.html#/{domain}/api/validate
-	BASE64 Encoder/Decoder: https://www.base64encode.org/
 * */
 public class ShaclValidationManager {
 
 	private static String VALIDATOR_URL = "http://localhost:8080/shacl/";
+	private final String TEXT_TURTLE = "text/turtle";
+	private final String JSON_FORMAT = "application/json";	// application/x-www-form-urlencoded
+	private final String STRING_FORMAT = "STRING";
+
 	private String ontologyToValidate;	// file:///home/davidgnabasik/dev/real_saref4auto/ontology/saref4auto.ttl or URL
+	private List<String> shaclFileList;
+	private List<RuleSet> ruleSetList;
 	private HttpClient client;
 	private ObjectMapper objectMapper;
-
-	//private String shaclRequestBody =
-	//		"{ \"contentToValidate\": \"ONTOLOGY_AS_BASE64_STRING\", \"embeddingMethod\": \"BASE64\", \"contentSyntax\": \"text/turtle\", \"reportSyntax\": \"application/json\", \"locale\": \"en\", \"rdfReportSyntax\": \"application/json\", \"externalRules\": [ { \"ruleSet\": \"SHACL_AS_BASE64_STRING\", \"embeddingMethod\": \"BASE64\", \"ruleSyntax\": \"text/turtle\" } ] }";
+	private ValidationRequest validationRequest;
 
 	private static String encodeBody(Object obj) {
 		return URLEncoder.encode(obj.toString(), StandardCharsets.UTF_8);
@@ -65,12 +69,78 @@ public class ShaclValidationManager {
 		http_exception, ioexception
 	}
 
+	class RuleSet {
+		private String ruleSet;	// JSON-encoded_SHACL_shape
+
+		public String getRuleSet() {
+			return ruleSet;
+		}
+		public void setRuleSet(String ruleSet) {
+			this.ruleSet = ruleSet;
+		}
+		// constants for now...
+		public String getEmbeddingMethod()	{ return STRING_FORMAT; }
+		public String getRuleSyntax() { return TEXT_TURTLE; }
+	}
+
+	class ValidationRequest {
+		private String contentToValidate;    // JSON-encoded ontology
+		private List<RuleSet> externalRules;
+		private Map<String, Object> properties;	// needed?
+
+		public String getContentToValidate() {
+			return contentToValidate;
+		}
+
+		public void setContentToValidate(String contentToValidate) {
+			this.contentToValidate = contentToValidate;
+		}
+
+		public Map<String, Object> getProperties() {
+			return properties;
+		}
+
+		public void setProperties(Map<String, Object> properties) {
+			this.properties = properties;
+		}
+
+		// constants for now...
+		public String getEmbeddingMethod() {
+			return STRING_FORMAT;
+		}
+
+		public String getContentSyntax() {
+			return TEXT_TURTLE;
+		}
+
+		public String getReportSyntax() {
+			return JSON_FORMAT;
+		}
+
+		public String getRdfReportSyntax() {
+			return JSON_FORMAT;
+		}
+
+		public String getLocale() {
+			return "en";
+		}
+
+		public List<RuleSet> getExternalRules() {
+			return externalRules;
+		}
+
+		public void setExternalRules(List<RuleSet> externalRules) {
+			this.externalRules = externalRules;
+		}
+
+	}
+
 	/**
 	 * Open a REST interface to the SHACL validator.
 	 */
 	public ShaclValidationManager(String ontologyToValidate) throws IOException {
-		client = HttpClient.newHttpClient();
-		objectMapper = new ObjectMapper();
+		this.client = HttpClient.newHttpClient();
+		this.objectMapper = new ObjectMapper();
 		this.ontologyToValidate = ontologyToValidate;
 		String url = System.getenv("VALIDATOR_URL");
 		if (url != null)  VALIDATOR_URL = url;
@@ -94,19 +164,49 @@ public class ShaclValidationManager {
 	}
 
 	/**
-	 * Preferred validation format is BASE64. Read file; return single BASE64-encoded string.
+	 * Read shacl files. Assign this.shaclFileList, this.ruleSetList.
+	 * Preferred validation format is JSON-escaped text. Requires \r\n as line breaks!!!
+	 */
+	private void createRuleSetList(List<String> shaclFileList)  {
+		this.shaclFileList = new ArrayList();
+		this.ruleSetList = new ArrayList();
+
+		for (int i = 0; i < shaclFileList.size(); i++) {
+			String readingFile = shaclFileList.get(i);
+			try {
+				String fileStr = new String(Files.readAllBytes(Paths.get(readingFile)));
+				RuleSet ruleSet = new RuleSet();
+				ruleSet.setRuleSet(fileStr); //.replaceAll("[\n]","\r\n"));
+				this.shaclFileList.add(readingFile);
+				this.ruleSetList.add(ruleSet);
+			} catch (IOException ex) {
+				System.out.println("ShaclValidationManager unable to read SHACL file: " + readingFile);
+			}
+		}
+	}
+
+	/**
+	 * Assign ValidationRequest object.
+	 * Preferred validation format is JSON-escaped text. Requires \r\n as line breaks!!!
 	 * @throws SAREFPipelineException
 	 */
-	public static String FormatAsBase64(String ontologyFile) throws SAREFPipelineException {
+	private void createValidationRequest(List<String> shaclFileList) throws SAREFPipelineException {
+		createRuleSetList(shaclFileList);
+		if (this.ruleSetList.size() < 1) {
+			throw new SAREFPipelineException("ShaclValidationManager", "No SHACL files to process!");
+		}
+		// process ontology file
 		try {
-			String value = Files.readString(Path.of(ontologyFile));  // 2Gb file size limit.
-			return Base64.getUrlEncoder().encodeToString(value.getBytes());
+			String fileStr = new String(Files.readAllBytes(Paths.get(this.ontologyToValidate)));
+			this.validationRequest = new ValidationRequest();
+			this.validationRequest.setContentToValidate(fileStr); // .replaceAll("[\n]","\r\n"));
+			this.validationRequest.setExternalRules(this.ruleSetList);
 		} catch (IOException ex) {
-			throw new SAREFPipelineException("FormatAsBase64", "Unable to format file as base64: " + ontologyFile);
+			throw new SAREFPipelineException("ShaclValidationManager", "Unable to read ontology file: " + this.ontologyToValidate);
 		}
 	}
 
-	public static HttpRequest.BodyPublisher ofForm(Map<String, Object> data) {
+	private HttpRequest.BodyPublisher ofForm(Map<String, Object> data) {
 		StringBuilder body = new StringBuilder();
 		for (Object dataKey : data.keySet()) {
 			if (body.length() > 0) {
@@ -121,46 +221,30 @@ public class ShaclValidationManager {
 
 	/**
 	 * POST JSON response format:
-	 {
-	 "date": "2024-04-05T10:18:24.197+0000",
-	 "result": "SUCCESS",
-	 "overview": {
-	 "profileID": "Clause_9_4_3_1"
-	 },
-	 "counters": {
-	 "nrOfAssertions": 0,
-	 "nrOfErrors": 0,
-	 "nrOfWarnings": 0
-	 },
-	 "context": {},
-	 "reports": {},
-	 "name": "SHACL Validation"
-	 }
-
-	 * Generic validator option: 1. Replace {contentToValidate} value with the ontology to validate encoded in BASE64. (This can aos be done with URLs.)
-	 * 2. Configure the user-provided SHACL shape as a RuleSet element of the externalRules array. The content of each RuleSet is as follows:
-	 * [ "ruleSet": "BASE64-encoded_SHACL_shape", "embeddingMethod":"BASE64", "ruleSyntax": "text/turtle" ]   We run one SHACL shape at a time.
-	 * POST request to Validate a single RDF instance.
+	 LIST OF: @prefix :        <https://saref.etsi.org/saref4auto/> .
+	 [ rdf:type     sh:ValidationReport ;
+	 	sh:conforms  true
+	 ] .
+	 * Generic validator option: 1. Replace {contentToValidate} value with the ontology to validate encoded in JSON. This can also be done with URLs.
+	 * 2. Configure the user-provided SHACL shape as a RuleSet element of the externalRules array.
+	 * [ "ruleSet": "JSON-encoded_SHACL_shape", "embeddingMethod":"STRING", "ruleSyntax": TEXT_TURTLE ]
+	 * POST request to Validate a single RDF ontology.
+	 * @throws SAREFPipelineException
 	 * @throws IOException
 	 * @throws InterruptedException
 	 */
-	public HttpResponse<String> validateOntologyWithShacl(String shaclFile) throws SAREFPipelineException, InterruptedException {
+	public HttpResponse<String> ValidateOntologyWithShacl(List<String> shaclFileList) throws SAREFPipelineException, InterruptedException {
 		try {
-			String ontologyBase64String = FormatAsBase64(this.ontologyToValidate);
-			String shaclBase64String = FormatAsBase64(shaclFile);
-			// populate shaclRequestBody json struct to map (no TypeReference)
-			String shaclRequestBody = "{ \"contentToValidate\": \"" + ontologyBase64String +
-				"\", \"embeddingMethod\": \"BASE64\", \"contentSyntax\": \"text/turtle\", \"reportSyntax\": \"application/json\", \"locale\": \"en\", \"rdfReportSyntax\": \"application/json\", \"externalRules\": [ { \"ruleSet\": \"" +
-					shaclBase64String + "\", \"embeddingMethod\": \"BASE64\", \"ruleSyntax\": \"text/turtle\" } ] }";
-			byte[] mapData = shaclRequestBody.getBytes();
-			Map<String,Object> myMap = objectMapper.readValue(mapData, HashMap.class);
-			// now update JSON data
-			//myMap.put("contentToValidate", ontologyBase64String);
-			//myMap.put("ruleSet", shaclBase64String);
+			createValidationRequest(shaclFileList);
+
+			String jsonStr = this.objectMapper.writeValueAsString(this.validationRequest);
+			String escapedJson = StringEscapeUtils.escapeJson(jsonStr);
+			System.out.println(escapedJson);//<<<
+
 			HttpRequest request = HttpRequest.newBuilder()
-					.header("Content-Type", "text/turtle")    // application/x-www-form-urlencoded
-					.uri(URI.create(VALIDATOR_URL + "any/upload"))
-					.POST(ofForm(myMap))
+					.header("Content-Type", JSON_FORMAT)
+					.uri(URI.create(VALIDATOR_URL + "any/upload"))	// any/api/validate
+					.POST(HttpRequest.BodyPublishers.ofString(jsonStr)) // escapedJson
 					.build();
 
 			HttpResponse<String> response = client.send(request, HttpResponse.BodyHandlers.ofString());
@@ -168,7 +252,7 @@ public class ShaclValidationManager {
 			System.out.println("\n Body: " + response.body());
 			return response;
 		} catch (IOException ex) {
-			throw new SAREFPipelineException("validateOntologyWithShacl", "Unable to process SHACL file: " + shaclFile);
+			throw new SAREFPipelineException("ValidateOntologyWithShacl", "Unable to validate ontology: " + this.ontologyToValidate);
 		}
 	}
 

src/main/resources/messages/Clause_9_4_6_Checker.properties

+server_unavailable=The validation server is unavailable at `%s`
+ioexception=Error while accessing the local file system
+missing=The shacl directory should contain at least one file. This file shall conform to the pattern specification as defined in clause 9.4.6 in TS 103 673.
+one=If a shacl directory exists, it should contain at least one shapes.ttl file.