Merge branch 'SalvaBranch2' into 'master'

Solved Themis and OOPS problems

See merge request saref/saref-pipeline!9

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

@@ -26,6 +26,8 @@
 package fr.emse.gitlab.saref.checkers;
 
 import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileWriter;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
@@ -129,9 +131,10 @@ public class Clause_9_4_5_Checker extends AbstractClauseChecker {
 		onto = out.toString().replaceAll("]]", "] ]");
 
 		String xmlRequest = "<?xml version='1.0' encoding='UTF-8'?>" + "<OOPSRequest>" + "<OntologyURI></OntologyURI>"
-				+ "<OntologyContent><![CDATA[" + onto + "]]></OntologyContent>" + "<Pitfalls>10</Pitfalls>"
+				+ "<OntologyContent><![CDATA[" + onto + "]]></OntologyContent>" + "<Pitfalls></Pitfalls>"
 				+ "<OutputFormat>RDF/XML</OutputFormat>" + "</OOPSRequest>";
 
+
 		Object[] arrayData = new Object[0];
 
 		try {
@@ -153,13 +156,10 @@ public class Clause_9_4_5_Checker extends AbstractClauseChecker {
 			String result = response.body().string();
 
 			String[] results = result.split("\\n");
+
 			List<String> pureData = new ArrayList<String>();
 			for (int i = 0; i < results.length; i++) {
-				if (results[i].startsWith("<")) {
-					for (int j = i; j < results.length; j++) {
-						pureData.add(results[j]);
-					}
-				}
+				pureData.add(results[i]);
 			}
 
 			arrayData = pureData.toArray(); // response into array
@@ -174,10 +174,11 @@ public class Clause_9_4_5_Checker extends AbstractClauseChecker {
 
 		int s = 0;
 
+
 		ArrayList<String> results = new ArrayList<String>();
 
 		while (s < count) {
-			String data = result.get(0).get(s) + result.get(1).get(s) + result.get(2).get(s);
+			String data = result.get(0).get(s).concat("-") + result.get(1).get(s).concat(".") + result.get(2).get(s) + "Affected Elements: " + result.get(3).get(s);
 			results.add(data);
 			s++;
 		}

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

@@ -25,11 +25,7 @@
  */
 package fr.emse.gitlab.saref.checkers;
 
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.StringWriter;
+import java.io.*;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.FileSystems;
 import java.nio.file.PathMatcher;
@@ -64,7 +60,7 @@ import okhttp3.Response;
 
 /**
  * Checks TS 103 673 Clause 9.5: Ontology tests
- * 
+ *
  */
 public class Clause_9_5_Checker extends AbstractClauseChecker {
 
@@ -140,6 +136,7 @@ public class Clause_9_5_Checker extends AbstractClauseChecker {
 		StringWriter requirementsRDFXML = new StringWriter();
 		version.getRequirements().write(requirementsRDFXML);
 
+
 		OkHttpClient httpClient = new OkHttpClient().newBuilder().build();
 		MediaType mediaType = MediaType.parse("application/json");
 		String jsonRequest = "{\"ontologiesCode\":[\""
@@ -147,9 +144,11 @@ public class Clause_9_5_Checker extends AbstractClauseChecker {
 				+ "\"]," + "\"testfile\":[\"" + requirementsRDFXML.toString().replaceAll("\\\"", "\\\\\"")
 						.replaceAll("\"", "\\\"").replaceAll("\t", " ")
 				+ "\"]," + "\"format\":\"junit\"}";
+
 		RequestBody body = RequestBody.create(jsonRequest, mediaType);
 		Request request = new Request.Builder().url("http://themis.linkeddata.es/rest/api/results").method("POST", body)
 				.addHeader("accept", "application/json").addHeader("Content-Type", "application/json").build();
+
 		try {
 			Response response = httpClient.newCall(request).execute();
 			if (response.code() != 200) {
@@ -164,12 +163,13 @@ public class Clause_9_5_Checker extends AbstractClauseChecker {
 				org.w3c.dom.Node node = nodeList.item(temp);
 				if (node.getNodeType() == org.w3c.dom.Node.ELEMENT_NODE) {
 					Element element = (Element) node;
-					String id = element.getAttributeNode("id").toString();
-					String name = element.getAttributeNode("name").toString();
-					String message = ((Element) node).getElementsByTagName("error").item(0).getAttributes()
-							.getNamedItem("message").toString();
-					String themisError = String.format("%s, %s, %s", id, name, message);
-					themisErrors.add(themisError);
+					if (((Element) node).getElementsByTagName("error").item(0) != null) {
+						String id = element.getAttributeNode("id").toString();
+						String name = element.getAttributeNode("name").toString();
+						String message = ((Element) node).getElementsByTagName("error").item(0).getAttributes().getNamedItem("message").toString();
+						String themisError = String.format("%s, %s, %s", id, name, message);
+						themisErrors.add(themisError);
+					}
 				}
 			}
 			if (!themisErrors.isEmpty()) {

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

@@ -33,13 +33,20 @@ public class OopsManager {
 		ArrayList<String> getID = new ArrayList<String>();
 		ArrayList<String> getName = new ArrayList<String>();
 		ArrayList<String> getInfo = new ArrayList<String>();
+		ArrayList<String> affectedElements = new ArrayList<String>();
+
 		ArrayList<ArrayList<String>> elements = new ArrayList<ArrayList<String>>();
 		elements.add(getID);
 		elements.add(getName);
 		elements.add(getInfo);
+		elements.add(affectedElements);
+
+		String affected = "";
 
 		for (int i = 0; i < data.length; i++) {
 			String data2 = data[i].toString().replaceAll("  ", "");
+
+
 			if (data2.startsWith("<oops:hasCode")) {
 				String[] data3 = data2.split("(<|>)");
 				getID.add(data3[2]);
@@ -53,6 +60,30 @@ public class OopsManager {
 				getInfo.add(data3[2]);
 				elements.set(2, getInfo);
 			}
+			if (i>0 && i < data.length-1) {
+				String prove = data[i - 1].toString().replaceAll("  ", "");
+				String prove2 = data[i + 1].toString().replaceAll("  ", "");
+
+				if (data2.startsWith("<oops:hasAffectedElement")) {
+					if (!prove.startsWith("<oops:hasAffectedElement")) {
+						String[] data3 = data2.split("(<|>)");
+						affected += data3[2];
+					}
+					else if (!prove2.startsWith("<oops:hasAffectedElement")){
+						String[] data3 = data2.split("(<|>)");
+						affected += ", " + data3[2];
+						affectedElements.add(affected);
+						elements.set(3, affectedElements);
+						affected = "";
+					}
+					else{
+						String[] data3 = data2.split("(<|>)");
+						affected += ", " + data3[2];
+					}
+				}
+
+			}
+
 		}
 
 		return elements;

src/main/resources/messages/Clause_9_5_Checker.properties

 missing=The `tests` directory should contain a file `tests.csv`. This file shall conform to the requirements specification as defined in clause 9.5.2 in TS 103 673.
 line=The `tests` specification shall be a CSV (Comma-Separated Values) file encoded in UTF-8. The first line of the file shall be the following: `Id;Requirement;Category;Test`
 ioexception=Error while checking the `tests` directory
-themis=OOPS found some problems. Violations are: %s
+themis=Themis found some problems. Violations are: %s
 themisError=Themis error. The service may be under maintenance.
\ No newline at end of file