Merge branch 'master' of https://github.com/OpenReqEU/cross-reference…

…-detection

pom.xml

@@ -41,6 +41,11 @@
 			<artifactId>spring-boot-starter-tomcat</artifactId>
 			<scope>provided</scope>
 		</dependency>
+		<dependency>
+		<groupId>javax.xml.bind</groupId>
+		<artifactId>jaxb-api</artifactId>
+		<version>2.3.1</version>
+		</dependency>
 		<!-- <dependency>
 			<groupId>org.springframework.boot</groupId>
 			<artifactId>spring-boot-starter-jdbc</artifactId>
@@ -97,6 +102,7 @@
 		<dependency>
 			<groupId>com.h2database</groupId>
 			<artifactId>h2</artifactId>
+			<scope>runtime</scope>
 		</dependency>
 
 		<!-- Jackson -->

src/main/java/com/essi/dependency/components/Bug.java

@@ -28,12 +28,6 @@ public Bug(String id, String summary, String description, List<String> comments)
         this.comments = comments;
     }
 
-    public Bug(List<String> components) {
-        this.id = components.get(0);
-        this.summary = components.get(1);
-        this.description = components.get(2);
-    }
-
     public String getId() {
 	return id;
     }
@@ -46,26 +40,10 @@ public String getDescription() {
 	return description;
     }
 
-    public void setSummary(String summary) {
-	this.summary = summary;
-    }
-
-    public void setDescription(String description) {
-	this.description = description;
-    }
-
-    public void setId(String id) {
-        this.id = id;
-    }
-
     public List<String> getComments() {
         return comments;
     }
 
-    public void setComments(List<String> comments) {
-        this.comments = comments;
-    }
-
     @Override
     public String toString() {
 	return "Bug [id=" + id + ",\n summary=" + summary + ",\n description=" + description

src/main/java/com/essi/dependency/components/Clause.java

@@ -32,18 +32,6 @@ public Clause(String doc, String vol, String part, String sect, String subsect,
 	this.id = id;
     }
 
-    public Clause(List<String> components) {
-	this.id = Integer.parseInt(components.get(0));
-	this.clauseString = components.get(1);
-	this.doc = components.get(2);
-	this.vol = components.get(3);
-	this.part = components.get(4);
-	this.sect = components.get(5);
-	this.subsect = components.get(6);
-	this.parag = components.get(7);
-	this.subparg = components.get(8);
-    }
-
     @ApiModelProperty(value = "Document")
     public String getDoc() {
 	return doc;

src/main/java/com/essi/dependency/components/DependencyType.java

@@ -16,35 +16,4 @@ public enum DependencyType {
     CROSS_REFERENCE, @JsonProperty("external-cross-reference")
     EXTERNAL_CROSS_REFERENCE;
 
-    public DependencyType find(String elem) {
-	switch (elem.toUpperCase()) {
-	case "CONTRIBUTES":
-	    return DependencyType.CONTRIBUTES;
-	case "DAMAGES":
-	    return DependencyType.DAMAGES;
-	case "REFINES":
-	    return DependencyType.REFINES;
-	case "REQUIRES":
-	    return DependencyType.REQUIRES;
-	case "INCOMPATIBLE":
-	    return DependencyType.INCOMPATIBLE;
-	case "DECOMPOSITION":
-	    return DependencyType.DECOMPOSITION;
-	case "SIMILAR":
-	    return DependencyType.SIMILAR;
-	case "DUPLICATES":
-	    return DependencyType.DUPLICATES;
-	case "REPLACES":
-	    return DependencyType.REPLACES;
-	case "CROSS_REFERENCE":
-	    return DependencyType.CROSS_REFERENCE;
-	case "EXTERNAL_CROSS_REFERENCE":
-	    return DependencyType.EXTERNAL_CROSS_REFERENCE;
-	default:
-		//error
-		break;
-	}
-	return null;
-    }
-
 }

src/main/java/com/essi/dependency/controller/Controller.java

@@ -10,6 +10,7 @@
 import javax.servlet.http.HttpServletRequest;
 
 import com.essi.dependency.functionalities.JSONHandler;
+import com.essi.dependency.service.StorageException;
 import com.essi.dependency.util.Control;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.HttpStatus;
@@ -111,14 +112,9 @@ public ResponseEntity crossReferenceDetector(
 	    objN = jh.storeDependencies("", dependencies);
 	    node = jh.storeRequirements(objN, clauseList);
 	    node = jh.createProject(node, clauseList);
-	} catch (FileFormatException e) {
+	} catch (StorageException | FileFormatException e) {
 		// show the error with an entity format.
-	    LinkedHashMap<String, String> result = new LinkedHashMap<>();
-	    result.put("status", "500");
-	    result.put("error", "Internal Server Error");
-	    result.put("exception", e.toString());
-	    result.put("message", "The format file must be htm or html.");
-	    return new ResponseEntity<>(result, HttpStatus.INTERNAL_SERVER_ERROR);
+	    return createException(500,"Internal Server Error",e.toString(),"The format file must be htm or html.");
 	}
 
 	// Delete the input data file and folder.
@@ -200,33 +196,13 @@ public ResponseEntity crossReferenceDetector(
 	    objN = jh.storeRequirements(objN, clauseList);
 	    objN = jh.createProject(objN, clauseList);
 	} catch (FileFormatException e) {
-	    LinkedHashMap<String, String> result = new LinkedHashMap<>();
-	    result.put("status", "500");
-	    result.put("error", "Internal Server Error");
-	    result.put("exception", e.toString());
-	    result.put("message", "The format file must be htm or html.");
-	    return new ResponseEntity<>(result, HttpStatus.INTERNAL_SERVER_ERROR);
+	    return createException(500,"Internal Server Error",e.toString(),"The format file must be htm or html.");
 	} catch (IndexOutOfBoundsException e) {
-	    LinkedHashMap<String, String> result = new LinkedHashMap<>();
-	    result.put("status", "500");
-	    result.put("error", "Internal Server Error");
-	    result.put("exception", e.toString());
-	    result.put("message", "Index exceeds the bounds.");
-	    return new ResponseEntity<>(result, HttpStatus.INTERNAL_SERVER_ERROR);
+	    return createException(500,"Internal Server Error",e.toString(),"Index exceeds the bounds.");
 	} catch (NumberFormatException e) {
-	    LinkedHashMap<String, String> result = new LinkedHashMap<>();
-	    result.put("status", "500");
-	    result.put("error", "Internal Server Error");
-	    result.put("exception", e.toString());
-	    result.put("message", "The parameters 'n' and 'm' must be Integers.");
-	    return new ResponseEntity<>(result, HttpStatus.INTERNAL_SERVER_ERROR);
+	    return createException(500,"Internal Server Error",e.toString(),"The parameters 'n' and 'm' must be Integers.");
 	} catch (IllegalArgumentException e) {
-	    LinkedHashMap<String, String> result = new LinkedHashMap<>();
-	    result.put("status", "500");
-	    result.put("error", "Internal Server Error");
-	    result.put("exception", e.toString());
-	    result.put("message", "The parameter 'n' must be bigger than 0 and lower than 'm' ( 0 < n < m ).");
-	    return new ResponseEntity<>(result, HttpStatus.INTERNAL_SERVER_ERROR);
+	    return createException(500,"Internal Server Error",e.toString(),"The parameter 'n' must be bigger than 0 and lower than 'm' ( 0 < n < m ).");
 	}
 	return new ResponseEntity<>(objN, HttpStatus.OK);
     }
@@ -278,13 +254,7 @@ public ResponseEntity crossReferenceDetectorJson(
 	    List<List<String>> clauseList = jh.readRequirement(depService.getJson(), projectId);
 	    depService.storeClauseList(clauseList);
 	} catch (Exception e) {
-		Control.getInstance().showErrorMessage(e.getMessage());
-	    LinkedHashMap<String, String> result = new LinkedHashMap<>();
-	    result.put("status", "500");
-	    result.put("error", "Internal Server Error");
-	    result.put("exception", e.toString());
-	    result.put("message", "");
-	    return new ResponseEntity<>(result, HttpStatus.INTERNAL_SERVER_ERROR);
+	    return createException(500,"Internal Server Error",e.toString(),"");
 
 	}
 
@@ -354,12 +324,7 @@ public ResponseEntity crossReferenceDetectorJson(
 	    List<List<String>> clauseList = jh.readRequirement(depService.getJson(), projectId);
 	    depService.storeClauseList(clauseList);
 	} catch (Exception e) {
-	    LinkedHashMap<String, String> result = new LinkedHashMap<>();
-	    result.put("status", "500");
-	    result.put("error", "Internal Server Error");
-	    result.put("exception", e.toString());
-	    result.put("message", "");
-	    return new ResponseEntity<>(result, HttpStatus.INTERNAL_SERVER_ERROR);
+	    return createException(500,"Internal Server Error",e.toString(),"");
 
 	}
 
@@ -376,4 +341,13 @@ public ResponseEntity<?> handleStorageFileNotFound(StorageFileNotFoundException
 	return ResponseEntity.notFound().build();
     }
 
+    private ResponseEntity createException(int status, String error, String exception, String message) {
+		LinkedHashMap<String, String> result = new LinkedHashMap<>();
+		result.put("status", status+"");
+		result.put("error", error);
+		result.put("exception", exception);
+		result.put("message", message);
+		return new ResponseEntity<>(result, HttpStatus.valueOf(status));
+	}
+
 }

src/main/java/com/essi/dependency/functionalities/ClauseExtraction.java

@@ -266,42 +266,4 @@ private void extractClauses(List<Object> clauseList, String line, String doc, St
 	    }
 	}
     }
-
-    /**
-     * Write the expressions (clauses, bugs) into an external document.
-     * 
-     * @param filename
-     * @param printID
-     * @throws IOException
-     */
-    public void writeClauses(String filename, Boolean printID) throws IOException {
-	try(BufferedWriter outputWriter =  new BufferedWriter(new FileWriter(filename))) {
-		for (Object c : clauseList) {
-			if (printID) {
-				outputWriter.write(((Clause) c).getId() + "- ");
-			}
-			outputWriter.write(((Clause) c).printMe());
-			outputWriter.write("\n");
-			outputWriter.newLine();
-		}
-		outputWriter.flush();
-	}
-    }
-
-    /**
-     * Write all list into an external document.
-     * 
-     * @param filename
-     * @param list
-     * @throws IOException
-     */
-    public <T> void writeList(String filename, List<T> list) throws IOException {
-	try(BufferedWriter outputWriter = new BufferedWriter(new FileWriter(filename))) {
-		for (T object : list) {
-			outputWriter.write(object.toString());
-			outputWriter.newLine();
-		}
-		outputWriter.flush();
-	}
-    }
 }

src/main/java/com/essi/dependency/functionalities/Grammar.java

@@ -212,7 +212,7 @@ public List<Object> applyGrammar(com.essi.dependency.components.Grammar grammarO
 				dep = (ArrayList<Object>) task.get(30, TimeUnit.SECONDS);
 
 			} catch (Exception e) {
-				Control.getInstance().showErrorMessage("[EXCEPTION] " + e + ": " + ((Bug) expression).toString());
+				Control.getInstance().showErrorMessage("[EXCEPTION] " + e.getMessage());
 			}
 
 			executor.shutdown();
@@ -488,7 +488,7 @@ public List<Object> resolvingCrossReference(Clause clause, Matcher matcher, List
 					} else if (terms[i + 1].matches(markerTerm)) {
 						tmpNextTerm = terms[i + 2].replaceAll("\\(|\\)", "");
 					}
-					if (tmpNextTerm.matches("\\d+(\\.\\d(\\.)?)*")) {
+					if (tmpNextTerm.matches("\\d+(\\.\\d(\\.)?)*") && currentLoc!=-1) {
 						String tail = "";
 						String head = "";
 						String point = "";

src/main/java/com/essi/dependency/service/DependencyService.java

@@ -55,14 +55,6 @@ public String getJson() {
 		return json;
 	}
 
-	public String getFilename() {
-		return this.filename;
-	}
-
-	public String getFilenamePath() {
-		return load(this.filename).toString();
-	}
-
 	/**
 	 * Store requirements into the list
 	 * @param clauseList
@@ -95,7 +87,7 @@ public void storeClauseList(List<List<String>> clauseList) {
 	 * 
 	 * @param file
 	 */
-	public void store(MultipartFile file) {
+	public void store(MultipartFile file) throws StorageException {
 		this.filename = StringUtils.cleanPath(file.getOriginalFilename());
 		try {
 			if (file.isEmpty()) {

src/main/java/com/essi/dependency/service/FileFormatException.java

@@ -6,20 +6,4 @@ public FileFormatException() {
 	super();
     }
 
-    public FileFormatException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
-	super(message, cause, enableSuppression, writableStackTrace);
-    }
-
-    public FileFormatException(String message, Throwable cause) {
-	super(message, cause);
-    }
-
-    public FileFormatException(String message) {
-	super(message);
-    }
-
-    public FileFormatException(Throwable cause) {
-	super(cause);
-    }
-
 }