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src/main/java/fr/mines_stetienne/ci/saref/checkers/Clause_9_4_6_Checker.java
View file @ 3fe37802
......@@ -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
View file @ 3fe37802
......@@ -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 0 → 100644
View file @ 3fe37802
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.