Worked on ShaclValidationManager.

docker.SHACL.validation.configuration.md

+docker.SHACL.validation.configuration.txt::
+
+SHACL Validation server notes: See ShaclValidationManager.java
+ Support per validation type of loading the imports defined in the input that can also be set by users at validation time.
+ Support for querying SPARQL endpoints to retrieve the content to validate.
+ Remote SHACL shape caching: Caching is used to avoid constant lookups of remote SHACL shape files. 
+ Once loaded, remote SHACL shape files will be automatically refreshed every hour.
+
+Docker development configuration::https://www.itb.ec.europa.eu/docs/guides/latest/installingTheTestBed/
+These steps are for the specific validator, not the generic one that is in actual use.
+Step 1: Install Docker Community Edition & Docker Compose from https://docs.docker.com/desktop/install/ubuntu/
+    docker --version => Docker version 26.0.0, build 2ae903e
+    docker compose version => Docker Compose version v2.25.0
+Step 2: Define the test bed’s configuration:
+    mkdir ~/dev/testbed && cd ~/dev/testbed && touch docker-compose.yml 
+    sudo groupadd docker && sudo usermod -aG docker ${USER} && sudo chmod 666 /var/run/docker.sock
+    sudo ufw allow 8080/tcp && sudo ufw status verbose   (Later: sudo netstat -lnp --tcp --udp)
+Step 3:     REST interface: http://localhost:8080/shacl/DOMAIN/api/validate    DOMAIN={Commodity|Ontology} 
+    Parameter   Verb    Description                                                         Example
+    validate    POST    Validate one RDF instance. Request payload type: application/json.  http://localhost:8080/shacl/Ontology/api/validate <payload>
+Step 4: Test your installation: browse to http://localhost:9000/    => test@test.com / test => })cdVZP8>=}wZFa  <adminPassword>
+Step 5: Docker commands to manage the test bed: 
+    docker build -t local/OntologyValidator .                                   # this binds the specific validator to the shapes configuration. NOT USED!
+    docker run -d --name SAREFvalidator -p 8080:8080 isaitb/shacl-validator     # this runs the general validator.
+
+
+Generic Validator Dockerfile::
+FROM isaitb/shacl-validator:latest
+COPY resources /validator/resources/
+ENV validator.resourceRoot /validator/resources/
+
+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
+Use Swagger UI for testing: http://localhost:8080/shacl/swagger-ui/index.html#/{domain}/api/validate
+                            http://localhost:8080/shacl/swagger-ui.html 
+
+~/dockerls.sh: sudo docker image ls && sudo docker volume ls && sudo docker container ls && sudo docker network ls
+    !!! images !!!
+    REPOSITORY                TAG       IMAGE ID       CREATED       SIZE
+    local/ontologyvalidator   latest    8b929e2a947c   3 hours ago   436MB  # THIS ONE IS NOT USED!
+    isaitb/shacl-validator    latest    723eca0b679b   2 weeks ago   436MB  # THIS ONE IS USED!
+    !!! volumes !!!
+    DRIVER    VOLUME NAME
+    !!! containers !!!
+    CONTAINER ID   IMAGE                     COMMAND                  CREATED       STATUS       PORTS                                       NAMES
+    d9daf40eed08   local/ontologyvalidator   "java -XX:+ExitOnOut…"   3 hours ago   Up 3 hours   0.0.0.0:8080->8080/tcp, :::8080->8080/tcp   SAREFvalidator
+    !!! networks !!!
+    NETWORK ID     NAME      DRIVER    SCOPE
+    4a98c5692963   bridge    bridge    local
+    f02e9cbf7d1d   host      host      local
+    631ce42d72e6   none      null      local
+
+

src/main/java/fr/mines_stetienne/ci/saref/checkers/Clause_10_1_Checker.java

@@ -60,7 +60,7 @@ public class Clause_10_1_Checker extends AbstractClauseChecker {
 		}
 		try {
 			if (Files.walk(dir.toPath(), 1).filter(p -> !p.toFile().isFile() && !p.toFile().getName().startsWith("."))
-					.count() != 1) {
+					.count() < 2) {  // count README.md
 				logError(getMessage(Clause_10_1_Checker.MESSAGE.one, repository.getProject().getOntologyFileName(Languages.TEXT_TURTLE)));
 			}
 		} catch (Exception ex) {

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

@@ -29,8 +29,8 @@ import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
-import java.net.http.HttpResponse;
 import java.nio.file.Files;
+import java.util.HashMap;
 import java.util.stream.Collectors;
 
 import fr.mines_stetienne.ci.saref.SAREFPipelineException;
@@ -47,7 +47,7 @@ import org.semanticweb.owlapi.model.OWLOntology;
 public class Clause_9_4_6_Checker extends AbstractClauseChecker {
 
 	private enum MESSAGE {
-		one, missing, ioexception, server_unavailable
+		one, missing, ioexception, server_unavailable, shacl_validation_failed
 	}
 
 	public Clause_9_4_6_Checker(RepositoryManager repositoryManager) throws SAREFPipelineException {
@@ -96,15 +96,27 @@ public class Clause_9_4_6_Checker extends AbstractClauseChecker {
 			logError(getMessage(Clause_9_4_6_Checker.MESSAGE.ioexception), e);
 		}
 
-		ShaclValidationManager.PingValidationServer();
-
-		//Map<String, HttpResponse<String>> responseMap = new HashMap<String, HttpResponse<String>>();
 		try {
+			ShaclValidationManager.PingValidationServer();
 			ShaclValidationManager shaclValidationManager = new ShaclValidationManager(ontologyToValidate);
-			HttpResponse<String> response = shaclValidationManager.ValidateOntologyWithShacl(shaclFileList);
-			//responseMap.put(shaclFileName, response);	// parse map for errors
+			HashMap<String, String> response = shaclValidationManager.ValidateOntologyWithShacl(shaclFileList);
+			if (!matchHashMap("200","true",response)) {
+				logError(getMessage(Clause_9_4_6_Checker.MESSAGE.shacl_validation_failed, ontologyToValidate));
+				throw new SAREFPipelineException(response.get("500"));
+			}
 		} catch (IOException | InterruptedException e) {
 			logError(getMessage(Clause_9_4_6_Checker.MESSAGE.ioexception, ontologyToValidate));
 		}
 	}
+
+	private boolean matchHashMap(String key, String value, HashMap<String, String> sG) {
+		if (sG != null){
+			if (sG.containsKey(key)){
+				if ((sG.get(key)).equals(value)){
+					return true;
+				}
+			}
+		}
+		return false;
+	}
 }
\ No newline at end of file

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

@@ -36,25 +36,26 @@ import java.nio.charset.StandardCharsets;
 import java.nio.file.Paths;
 import java.util.Map;
 import java.util.List;
+import java.util.HashMap;
 import java.util.ArrayList;
-//import java.util.HashMap;
-import org.apache.commons.lang3.StringEscapeUtils;
+//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 with Dockerfile
+/*	docker run -d --name SAREFvalidator -p 8080:8080 isaitb/shacl-validator	 # runs the generic validator locally given a  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
+	Use Swagger UI for testing: http://localhost:8080/shacl/swagger-ui/index.html#/{domain}/api/validate or http://193.49.174.57:4050/shacl/swagger-ui/index.html#
+	Online validator: https://www.itb.ec.europa.eu/shacl/any/upload
 * */
 public class ShaclValidationManager {
 
-	private static String VALIDATOR_URL = "http://localhost:8080/shacl/";
+	private static String VALIDATOR_URL = "http://localhost:8080/shacl/"; //"http://193.49.174.57:4050/shacl/";
 	private final String TEXT_TURTLE = "text/turtle";
-	private final String JSON_FORMAT = "application/json";	// application/x-www-form-urlencoded
+	private final String JSON_FORMAT = "application/json";
 	private final String STRING_FORMAT = "STRING";
 
-	private String ontologyToValidate;	// file:///home/davidgnabasik/dev/real_saref4auto/ontology/saref4auto.ttl or URL
+	private String ontologyToValidate;	// can be file or URL.
 	private List<String> shaclFileList;
 	private List<RuleSet> ruleSetList;
 	private HttpClient client;
@@ -86,7 +87,6 @@ public class ShaclValidationManager {
 	class ValidationRequest {
 		private String contentToValidate;    // JSON-encoded ontology
 		private List<RuleSet> externalRules;
-		private Map<String, Object> properties;	// needed?
 
 		public String getContentToValidate() {
 			return contentToValidate;
@@ -96,12 +96,12 @@ public class ShaclValidationManager {
 			this.contentToValidate = contentToValidate;
 		}
 
-		public Map<String, Object> getProperties() {
-			return properties;
+		public List<RuleSet> getExternalRules() {
+			return externalRules;
 		}
 
-		public void setProperties(Map<String, Object> properties) {
-			this.properties = properties;
+		public void setExternalRules(List<RuleSet> externalRules) {
+			this.externalRules = externalRules;
 		}
 
 		// constants for now...
@@ -114,29 +114,25 @@ public class ShaclValidationManager {
 		}
 
 		public String getReportSyntax() {
-			return JSON_FORMAT;
+			return TEXT_TURTLE;
 		}
 
 		public String getRdfReportSyntax() {
-			return JSON_FORMAT;
+			return TEXT_TURTLE;
 		}
 
 		public String getLocale() {
 			return "en";
 		}
 
-		public List<RuleSet> getExternalRules() {
-			return externalRules;
+		// TODO: set loadImports to true to allow recursive searches.
+		public boolean getLoadImports() {
+			return false;
 		}
-
-		public void setExternalRules(List<RuleSet> externalRules) {
-			this.externalRules = externalRules;
-		}
-
 	}
 
 	/**
-	 * Open a REST interface to the SHACL validator.
+	 * Open a REST interface to the remote SHACL validator.
 	 */
 	public ShaclValidationManager(String ontologyToValidate) throws IOException {
 		this.client = HttpClient.newHttpClient();
@@ -144,6 +140,7 @@ public class ShaclValidationManager {
 		this.ontologyToValidate = ontologyToValidate;
 		String url = System.getenv("VALIDATOR_URL");
 		if (url != null)  VALIDATOR_URL = url;
+		System.out.println("SHACL validation server running at "+VALIDATOR_URL);
 	}
 
 	/**
@@ -160,7 +157,6 @@ public class ShaclValidationManager {
 		} catch (IOException e) {
 			throw new SAREFPipelineException("response", "Unknown host: " + VALIDATOR_URL);
 		}
-		//logError(getMessage(ShaclValidationManager.MESSAGE.http_exception, VALIDATOR_URL));
 	}
 
 	/**
@@ -176,7 +172,7 @@ public class ShaclValidationManager {
 			try {
 				String fileStr = new String(Files.readAllBytes(Paths.get(readingFile)));
 				RuleSet ruleSet = new RuleSet();
-				ruleSet.setRuleSet(fileStr); //.replaceAll("[\n]","\r\n"));
+				ruleSet.setRuleSet(fileStr);
 				this.shaclFileList.add(readingFile);
 				this.ruleSetList.add(ruleSet);
 			} catch (IOException ex) {
@@ -199,7 +195,7 @@ public class ShaclValidationManager {
 		try {
 			String fileStr = new String(Files.readAllBytes(Paths.get(this.ontologyToValidate)));
 			this.validationRequest = new ValidationRequest();
-			this.validationRequest.setContentToValidate(fileStr); // .replaceAll("[\n]","\r\n"));
+			this.validationRequest.setContentToValidate(fileStr);
 			this.validationRequest.setExternalRules(this.ruleSetList);
 		} catch (IOException ex) {
 			throw new SAREFPipelineException("ShaclValidationManager", "Unable to read ontology file: " + this.ontologyToValidate);
@@ -219,8 +215,17 @@ public class ShaclValidationManager {
 		return HttpRequest.BodyPublishers.ofString(body.toString());
 	}
 
+	// Use 500 Internal server error for failed SHACL validation => value is SHACL file name OR error message.
+	private HashMap<String, String> parseHttpResponse(HttpResponse<String> response) {
+		String result = response.body().substring(response.body().indexOf("sh:conforms")+13);
+		result = result.substring(0,4).replaceAll("\\s+","");
+		HashMap<String, String> map = new HashMap<>();
+		map.put(String.valueOf(response.statusCode()), result);
+		return map;
+	}
+
 	/**
-	 * POST JSON response format:
+	 * POST JSON successful response format:
 	 LIST OF: @prefix :        <https://saref.etsi.org/saref4auto/> .
 	 [ rdf:type     sh:ValidationReport ;
 	 	sh:conforms  true
@@ -229,28 +234,30 @@ public class ShaclValidationManager {
 	 * 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.
+	 * Return <HTTP status code, validation result>.
 	 * @throws SAREFPipelineException
 	 * @throws IOException
 	 * @throws InterruptedException
 	 */
-	public HttpResponse<String> ValidateOntologyWithShacl(List<String> shaclFileList) throws SAREFPipelineException, InterruptedException {
+	public HashMap<String, String> ValidateOntologyWithShacl(List<String> shaclFileList) throws SAREFPipelineException, InterruptedException {
 		try {
 			createValidationRequest(shaclFileList);
 
 			String jsonStr = this.objectMapper.writeValueAsString(this.validationRequest);
-			String escapedJson = StringEscapeUtils.escapeJson(jsonStr);
-			System.out.println(escapedJson);//<<<
+			// Had to format the json manually because escapeJson() also escaped double-quotes. See validation_request_using_strings.txt
+			//String escapedJson = StringEscapeUtils.escapeJson(jsonStr);
+			jsonStr = jsonStr.replace("text/turtle", "text~turtle").replace("application/json", "application~json");
+			jsonStr = jsonStr.replace("/","\\/").replace("\\n","\\r\\n");
+			jsonStr = jsonStr.replace("text~turtle", "text/turtle").replace("application~json", "application/json");
 
 			HttpRequest request = HttpRequest.newBuilder()
 					.header("Content-Type", JSON_FORMAT)
-					.uri(URI.create(VALIDATOR_URL + "any/upload"))	// any/api/validate
-					.POST(HttpRequest.BodyPublishers.ofString(jsonStr)) // escapedJson
+					.uri(URI.create(VALIDATOR_URL + "any/api/validate"))
+					.POST(HttpRequest.BodyPublishers.ofString(jsonStr))
 					.build();
 
 			HttpResponse<String> response = client.send(request, HttpResponse.BodyHandlers.ofString());
-			System.out.println("Status code: " + response.statusCode()); //<<<
-			System.out.println("\n Body: " + response.body());
-			return response;
+			return parseHttpResponse(response);
 		} catch (IOException ex) {
 			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`
+shacl_validation_failed=SHACL validation failed for `%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.