Commit b2e5c160 authored by Maxime Lefrançois's avatar Maxime Lefrançois
Browse files

some corrections

parent 012f43d1

src/main/java/fr/emse/gitlab/saref/checkers/Clause_9_3_Checker.java

+8 −11
Original line number Original line Diff line number Diff line
@@ -32,6 +32,8 @@ import java.nio.file.Path; 
import java.util.Optional;

import java.util.Optional;

import java.util.stream.Collectors;

import java.util.stream.Collectors;





import org.apache.commons.io.FileUtils;



import fr.emse.gitlab.saref.SAREF;

import fr.emse.gitlab.saref.SAREF;

import fr.emse.gitlab.saref.SAREFPipelineException;

import fr.emse.gitlab.saref.SAREFPipelineException;

import fr.emse.gitlab.saref.managers.GenerateRDFaManager;

import fr.emse.gitlab.saref.managers.GenerateRDFaManager;
@@ -119,20 +121,15 @@ public class Clause_9_3_Checker extends AbstractClauseChecker { 
		});

		});

	}

	}





	private void requirementsRDFaGenerator() throws SAREFPipelineException{

	private void requirementsRDFaGenerator() throws SAREFPipelineException, IOException{

		String categoryChanger = "";

		String categoryChanger = "";

		String repoName = project.getName();

		String repoName = project.getName();

		String href = project.getNamespace();

		String href = project.getNamespace();





		File reqCSV = new File(repository.getDirectory(), "/requirements/requirements.csv");

		File reqCSV = new File(repository.getDirectory(), "/requirements/requirements.csv");



		File versionSite = new File(siteManager.siteDir, version.getVersionPath());

		File reqHTML = new File(repository.getDirectory(), "/target/site/requirements.html");

		FileUtils.forceMkdir(versionSite);



		File reqHTML = new File(versionSite, "requirements.html");

		GenerateRDFaManager manager = new GenerateRDFaManager();

		GenerateRDFaManager.GenerateRDFa(categoryChanger, repoName, href, reqCSV, reqHTML, "requirements");



		manager.GenerateRDFaManager(categoryChanger, repoName, href, reqCSV, reqHTML, "requirements");



	}

	}





}
 
}

src/main/java/fr/emse/gitlab/saref/checkers/Clause_9_4_5_Checker.java

+32 −47
Original line number Original line Diff line number Diff line
@@ -32,8 +32,6 @@ import java.util.List; 
import java.util.Set;

import java.util.Set;

import java.util.stream.Collectors;

import java.util.stream.Collectors;





import fr.emse.gitlab.saref.SAREFPipeline;

import fr.emse.gitlab.saref.managers.OopsManager;

import org.apache.jena.rdf.model.Model;

import org.apache.jena.rdf.model.Model;

import org.semanticweb.owl.explanation.api.Explanation;

import org.semanticweb.owl.explanation.api.Explanation;

import org.semanticweb.owl.explanation.api.ExplanationGenerator;

import org.semanticweb.owl.explanation.api.ExplanationGenerator;
@@ -44,9 +42,13 @@ import org.semanticweb.owlapi.profiles.OWLProfileReport; 




import fr.emse.gitlab.saref.SAREFPipelineException;

import fr.emse.gitlab.saref.SAREFPipelineException;

import fr.emse.gitlab.saref.managers.OntologyManager;

import fr.emse.gitlab.saref.managers.OntologyManager;

import fr.emse.gitlab.saref.managers.OopsManager;

import fr.emse.gitlab.saref.managers.RepositoryManager;

import fr.emse.gitlab.saref.managers.RepositoryManager;



import okhttp3.MediaType;

import okhttp3.*;

import okhttp3.OkHttpClient;

import okhttp3.Request;

import okhttp3.RequestBody;

import okhttp3.Response;





/**

/**

 * Checks TS 103 673 Clause 9.4.5: OWL Profile, Consistency, and Satisfiability

 * Checks TS 103 673 Clause 9.4.5: OWL Profile, Consistency, and Satisfiability
@@ -111,20 +113,11 @@ public class Clause_9_4_5_Checker extends AbstractClauseChecker { 




		Model model = version.getModel();

		Model model = version.getModel();

		model.write(out, "RDF/XML"); // write in string and then replace

		model.write(out, "RDF/XML"); // write in string and then replace

		onto = out.toString().replace("]]","] ]");

		onto = out.toString().replaceAll("]]", "] ]");



		String xmlRequest = "<?xml version='1.0' encoding='UTF-8'?>" +

				"<OOPSRequest>" +

				"<OntologyURI></OntologyURI>" +

				"<OntologyContent><![CDATA[" + onto + "]]></OntologyContent>" +

				"<Pitfalls>10</Pitfalls>" +

				"<OutputFormat>RDF/XML</OutputFormat>" +

				"</OOPSRequest>";







		String xmlRequest = "<?xml version='1.0' encoding='UTF-8'?>" + "<OOPSRequest>" + "<OntologyURI></OntologyURI>"

		OopsManager manager = new OopsManager();

				+ "<OntologyContent><![CDATA[" + onto + "]]></OntologyContent>" + "<Pitfalls>10</Pitfalls>"



				+ "<OutputFormat>RDF/XML</OutputFormat>" + "</OOPSRequest>";

		ArrayList<ArrayList<String>> res = new ArrayList<ArrayList<String>>();





		Object[] arrayData = new Object[0];

		Object[] arrayData = new Object[0];
@@ -136,21 +129,16 @@ public class Clause_9_4_5_Checker extends AbstractClauseChecker { 




			RequestBody body = RequestBody.create(xmlRequest, mediaType);

			RequestBody body = RequestBody.create(xmlRequest, mediaType);





			Request request = new Request.Builder()

			Request request = new Request.Builder().url("http://oops.linkeddata.es/rest").method("POST", body)

					.url("http://oops.linkeddata.es/rest")

					.addHeader("Content-Type", "application/xml").build();

					.method("POST", body)

					.addHeader("Content-Type", "application/xml")

					.build();





			Response response = httpClient.newCall(request).execute();

			Response response = httpClient.newCall(request).execute();







			String result = response.body().string();

			String result = response.body().string();







			String[] results = result.split("\\n");

			String[] results = result.split("\\n");

			List<String> pureData = new ArrayList<String>();

			List<String> pureData = new ArrayList<String>();

			for(int i=0; i<results.length-1;i++){

			for (int i = 0; i < results.length; i++) {

				if (results[i].startsWith("<")) {

				if (results[i].startsWith("<")) {

					for (int j = i; j < results.length; j++) {

					for (int j = i; j < results.length; j++) {

						pureData.add(results[j]);

						pureData.add(results[j]);
@@ -158,18 +146,15 @@ public class Clause_9_4_5_Checker extends AbstractClauseChecker { 
				}

				}

			}

			}







			arrayData = pureData.toArray(); // response into array

			arrayData = pureData.toArray(); // response into array





		}

		} catch (IOException e) {

		catch (IOException e) {

			logWarning(getMessage(MESSAGE.oopsError));

			log(getMessage(MESSAGE.oopsError), SAREFPipeline.Mode.RELEASE, SAREFPipeline.Mode.PORTAL);

		}

		}





		int count = OopsManager.counter(arrayData);





		int count = manager.counter(arrayData);

		ArrayList<ArrayList<String>> result = OopsManager.getData(arrayData);



		ArrayList<ArrayList<String>> result = manager.getData(arrayData);





		int s = 0;

		int s = 0;
@@ -181,11 +166,11 @@ public class Clause_9_4_5_Checker extends AbstractClauseChecker { 
			s++;

			s++;

		}

		}





		String printData = results.stream().map(e -> e.toString()).collect(Collectors.joining("\n- ", "\n\n- ", "\n\n"));

		String printData = results.stream().map(e -> e.toString())

				.collect(Collectors.joining("\n- ", "\n\n- ", "\n\n"));

		if (count != 0) {

		if (count != 0) {

			log(getMessage(MESSAGE.oops, printData), SAREFPipeline.Mode.RELEASE, SAREFPipeline.Mode.PORTAL);

			logWarning(getMessage(MESSAGE.oops, printData));

		}

		}

	}

	}







}
 
}

src/main/java/fr/emse/gitlab/saref/checkers/Clause_9_5_Checker.java

+66 −85
Original line number Original line Diff line number Diff line
@@ -25,21 +25,17 @@ 
 */

 */

package fr.emse.gitlab.saref.checkers;

package fr.emse.gitlab.saref.checkers;





import java.io.*;

import java.io.ByteArrayOutputStream;

import java.nio.file.*;

import java.io.File;

import java.io.IOException;

import java.nio.file.FileSystems;

import java.nio.file.Files;

import java.nio.file.Path;

import java.nio.file.PathMatcher;

import java.util.ArrayList;

import java.util.ArrayList;

import java.util.Optional;

import java.util.Optional;

import java.util.stream.Collectors;

import java.util.stream.Collectors;





import fr.emse.gitlab.saref.SAREFPipeline;

import fr.emse.gitlab.saref.SAREFPipelineException;

import fr.emse.gitlab.saref.entities.SAREFRepository;

import fr.emse.gitlab.saref.entities.SAREFVersion;

import fr.emse.gitlab.saref.managers.DatasetManager;

import fr.emse.gitlab.saref.managers.GenerateRDFaManager;

import fr.emse.gitlab.saref.managers.RepositoryManager;

import fr.emse.gitlab.saref.managers.ThemisManager;

import okhttp3.*;

import org.apache.any23.Any23;

import org.apache.any23.Any23;

import org.apache.any23.extractor.ExtractionException;

import org.apache.any23.extractor.ExtractionException;

import org.apache.any23.source.DocumentSource;

import org.apache.any23.source.DocumentSource;
@@ -47,11 +43,25 @@ import org.apache.any23.source.FileDocumentSource; 
import org.apache.any23.writer.RDFXMLWriter;

import org.apache.any23.writer.RDFXMLWriter;

import org.apache.any23.writer.TripleHandler;

import org.apache.any23.writer.TripleHandler;

import org.apache.any23.writer.TripleHandlerException;

import org.apache.any23.writer.TripleHandlerException;

import org.apache.commons.io.FileUtils;

import org.apache.jena.rdf.model.Model;

import org.apache.jena.rdf.model.Model;

import org.w3c.dom.Document;

import org.w3c.dom.Document;

import org.w3c.dom.Element;

import org.w3c.dom.Element;

import org.w3c.dom.NodeList;

import org.w3c.dom.NodeList;





import fr.emse.gitlab.saref.SAREFPipelineException;

import fr.emse.gitlab.saref.entities.SAREFRepository;

import fr.emse.gitlab.saref.entities.SAREFVersion;

import fr.emse.gitlab.saref.managers.DatasetManager;

import fr.emse.gitlab.saref.managers.GenerateRDFaManager;

import fr.emse.gitlab.saref.managers.RepositoryManager;

import fr.emse.gitlab.saref.managers.ThemisManager;

import okhttp3.MediaType;

import okhttp3.OkHttpClient;

import okhttp3.Request;

import okhttp3.RequestBody;

import okhttp3.Response;



/**

/**

 * Checks TS 103 673 Clause 9.5: Ontology tests

 * Checks TS 103 673 Clause 9.5: Ontology tests

 * 

 *
@@ -140,25 +150,16 @@ public class Clause_9_5_Checker extends AbstractClauseChecker { 
		});

		});

	}

	}







	public void checkThemis() throws SAREFPipelineException {

	public void checkThemis() throws SAREFPipelineException {

		try {

		File versionSite = new File(siteManager.siteDir, version.getVersionPath());



		File tHTML = new File(versionSite, "tests.html");

			File tHTML = new File(repository.getDirectory(),"target/site/tests.html");



			Any23 runner = new Any23();



			ByteArrayOutputStream out = new ByteArrayOutputStream();



		DocumentSource source = new FileDocumentSource(tHTML);

		DocumentSource source = new FileDocumentSource(tHTML);

			TripleHandler handler = new RDFXMLWriter(out);

		Any23 runner = new Any23();

		try(ByteArrayOutputStream out = new ByteArrayOutputStream(); TripleHandler handler = new RDFXMLWriter(out);) {

			runner.extract(source, handler);

			runner.extract(source, handler);





			handler.close();



			String xmlData = out.toString();

			String xmlData = out.toString();







			ArrayList<String[]> res = makeCall(xmlData, repository, datasetManager, version);

			ArrayList<String[]> res = makeCall(xmlData, repository, datasetManager, version);





			ArrayList<String> result = new ArrayList<String>();

			ArrayList<String> result = new ArrayList<String>();
@@ -168,29 +169,21 @@ public class Clause_9_5_Checker extends AbstractClauseChecker { 
				result.add(response);

				result.add(response);

			}

			}





			String data = result.stream().map(e -> e.toString()).collect(Collectors.joining("\n- ", "\n\n- ", "\n\n"));



			if (!res.isEmpty()) {

			if (!res.isEmpty()) {

				log(getMessage(MESSAGE.themis, data), SAREFPipeline.Mode.RELEASE, SAREFPipeline.Mode.RELEASE, SAREFPipeline.Mode.PORTAL);

				String data = result.stream().map(e -> e.toString()).collect(Collectors.joining("\n- ", "\n\n- ", "\n\n"));

				logWarning(getMessage(MESSAGE.themis, data));

			}

			}





		} catch (FileNotFoundException e) {

		} catch (ExtractionException | IOException | TripleHandlerException e) {

			e.printStackTrace();

			logWarning(getMessage(MESSAGE.themisError));

		} catch (ExtractionException | UnsupportedEncodingException e) {

			e.printStackTrace();

		} catch (IOException e) {

			log(getMessage(MESSAGE.themisError), SAREFPipeline.Mode.RELEASE, SAREFPipeline.Mode.RELEASE, SAREFPipeline.Mode.PORTAL);

		} catch (TripleHandlerException e) {

			e.printStackTrace();

		}

		}

	}

	}







	public ArrayList<String[]> makeCall(String xmlData, SAREFRepository repository, DatasetManager datasetManager,

	public ArrayList<String []> makeCall(String xmlData, SAREFRepository repository, DatasetManager datasetManager, SAREFVersion version)  throws SAREFPipelineException {

			SAREFVersion version) throws SAREFPipelineException {





		ArrayList<String[]> res = new ArrayList<String[]>();

		ArrayList<String[]> res = new ArrayList<String[]>();

		try{

		try (ByteArrayOutputStream out = new ByteArrayOutputStream()) {

			ByteArrayOutputStream out = new ByteArrayOutputStream();

			String onto = "";

			String onto = "";





			Model model = version.getModel();

			Model model = version.getModel();
@@ -201,30 +194,22 @@ public class Clause_9_5_Checker extends AbstractClauseChecker { 




			MediaType mediaType = MediaType.parse("application/json");

			MediaType mediaType = MediaType.parse("application/json");





			String jsonRequest = "{\"ontologiesCode\":[\"" +

			String jsonRequest = "{\"ontologiesCode\":[\""

					onto.replace("\\\"", "\\\\\"").replace("\"", "\\\"").replace("\t"," ") +

					+ onto.replaceAll("\\\"", "\\\\\"").replaceAll("\"", "\\\"").replaceAll("\t", " ") + "\"],"

					"\"]," + "\"testfile\":[\"" +

					+ "\"testfile\":[\"" + xmlData.replaceAll("\\\"", "\\\\\"").replaceAll("\"", "\\\"").replaceAll("\t", " ")

					xmlData.replace("\\\"", "\\\\\"").replace("\"", "\\\"").replace("\t"," ") +

					+ "\"]," + "\"format\":\"junit\"}";

					"\"]," + "\"format\":\"junit\"}";







			RequestBody body = RequestBody.create(jsonRequest, mediaType);

			RequestBody body = RequestBody.create(jsonRequest, mediaType);





			Request request = new Request.Builder()

			Request request = new Request.Builder().url("http://themis.linkeddata.es/rest/api/results")

					.url("http://themis.linkeddata.es/rest/api/results")

					.method("POST", body).addHeader("accept", "application/json")

					.method("POST", body)

					.addHeader("Content-Type", "application/json").build();

					.addHeader("accept", "application/json")

					.addHeader("Content-Type", "application/json")

					.build();





			Response response = httpClient.newCall(request).execute();

			Response response = httpClient.newCall(request).execute();







			String result = response.body().string();

			String result = response.body().string();





			ThemisManager manager = new ThemisManager();

			Document doc = ThemisManager.convertStringToXMLDocument(result);



			Document doc = manager.convertStringToXMLDocument(result);





			NodeList nodeList = doc.getElementsByTagName("testcase");

			NodeList nodeList = doc.getElementsByTagName("testcase");

			for (int temp = 0; temp < nodeList.getLength(); temp++) {

			for (int temp = 0; temp < nodeList.getLength(); temp++) {
@@ -234,34 +219,30 @@ public class Clause_9_5_Checker extends AbstractClauseChecker { 
					Element element = (Element) node;

					Element element = (Element) node;

					part[0] = "" + element.getAttributeNode("id");

					part[0] = "" + element.getAttributeNode("id");

					part[1] = "" + element.getAttributeNode("name");

					part[1] = "" + element.getAttributeNode("name");

					part[2] = ""+((Element) node).getElementsByTagName("error").item(0).getAttributes().getNamedItem("message");

					part[2] = "" + ((Element) node).getElementsByTagName("error").item(0).getAttributes()

							.getNamedItem("message");





					res.add(part);

					res.add(part);



				}

				}

			}

			}



		} catch (IOException e) {

		} catch (IOException e) {

			log(getMessage(MESSAGE.themisError), SAREFPipeline.Mode.RELEASE, SAREFPipeline.Mode.RELEASE, SAREFPipeline.Mode.PORTAL);

			logWarning(getMessage(MESSAGE.themisError));

		}

		}

		return res;

		return res;

	}

	}





	private void testsRDFaGenerator() throws SAREFPipelineException{

	private void testsRDFaGenerator() throws SAREFPipelineException, IOException {

		if(pipeline.ignoreSite) {

			return;

		}

		String categoryChanger = "";

		String categoryChanger = "";

		String repoName = project.getName();

		String repoName = project.getName();

		String href = project.getNamespace();

		String href = project.getNamespace();



		File testCSV = new File(repository.getDirectory(), "/tests/tests.csv");

		File testCSV = new File(repository.getDirectory(), "/tests/tests.csv");



		File versionSite = new File(siteManager.siteDir, version.getVersionPath());

		File testHTML = new File(repository.getDirectory(), "/target/site/tests.html");

		FileUtils.forceMkdir(versionSite);



		File testHTML = new File(versionSite, "tests.html");

		GenerateRDFaManager manager = new GenerateRDFaManager();

		GenerateRDFaManager.GenerateRDFa(categoryChanger, repoName, href, testCSV, testHTML, "tests");



		manager.GenerateRDFaManager(categoryChanger, repoName, href, testCSV, testHTML, "tests");



	}

	}







}
 
}

src/main/java/fr/emse/gitlab/saref/entities/SAREFNamedGraph.java

+1 −1
Original line number Original line Diff line number Diff line
@@ -45,7 +45,7 @@ public class SAREFNamedGraph { 
			return false;

			return false;

		if (getClass() != obj.getClass())

		if (getClass() != obj.getClass())

			return false;

			return false;

		SAREFTerm other = (SAREFTerm) obj;

		SAREFNamedGraph other = (SAREFNamedGraph) obj;

		if (iri == null) {

		if (iri == null) {

			if (other.iri != null)

			if (other.iri != null)

				return false;

				return false;

src/main/java/fr/emse/gitlab/saref/managers/GenerateRDFaManager.java

+178 −203

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