New function to extract metrics of a Java Repository

.gitignore

@@ -12,4 +12,3 @@ bin
 *.log
 
 *.jar
-metrics/

pom.xml

@@ -92,7 +92,7 @@
 		<dependency>
 			<groupId>org.slf4j</groupId>
 			<artifactId>slf4j-log4j12</artifactId>
-			<version>1.6.6</version>
+			<version>1.7.6</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>
@@ -175,25 +175,25 @@
 			<version>4.11</version>
 		</dependency>
 		<dependency>
-		        <groupId>org.gitective</groupId>
-		        <artifactId>gitective-core</artifactId>
-		        <version>0.9.9</version>
-		</dependency>
-		<dependency>
-		        <groupId>org.mongodb</groupId>
-		        <artifactId>mongo-java-driver</artifactId>
-		        <version>2.11.3</version>
+	        <groupId>org.mongodb</groupId>
+	        <artifactId>mongo-java-driver</artifactId>
+	        <version>2.11.3</version>
 		 </dependency>
 		 <dependency>
-		        <groupId>org.mongodb.morphia</groupId>
-		        <artifactId>morphia</artifactId>
-		        <version>0.105</version>
+	        <groupId>org.mongodb.morphia</groupId>
+	        <artifactId>morphia</artifactId>
+	        <version>0.105</version>
 		 </dependency>
 		 <dependency>
-			    <groupId>de.flapdoodle.embed</groupId>
-			    <artifactId>de.flapdoodle.embed.mongo</artifactId>
-			    <version>1.42</version>
-			</dependency>
+			<groupId>org.eclipse.jdt</groupId>
+			<artifactId>org.eclipse.jdt.core</artifactId>
+			<version>3.7.1</version>
+		</dependency>
+		 <dependency>
+		    <groupId>de.flapdoodle.embed</groupId>
+		    <artifactId>de.flapdoodle.embed.mongo</artifactId>
+		    <version>1.40</version>
+		</dependency>
 	</dependencies>
 
 	<build>
@@ -247,6 +247,7 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-source-plugin</artifactId>
+				<version>2.2.1</version>
 				<executions>
 					<execution>
 						<id>attach-sources</id>
@@ -260,6 +261,7 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-javadoc-plugin</artifactId>
+				<version>2.9.1</version>
 				<executions>
 					<execution>
 						<id>attach-javadocs</id>
@@ -287,7 +289,7 @@
 						</goals>
 					</execution>
 				</executions>
-			</plugin>
+			</plugin>			
 		</plugins>
 	</build>
 </project>

src/java/main/br/ufpe/cin/groundhog/database/GroundhogDB.java

@@ -4,6 +4,7 @@
 
 import org.mongodb.morphia.Datastore;
 import org.mongodb.morphia.Morphia;
+import org.mongodb.morphia.Key;
 
 import br.ufpe.cin.groundhog.GitHubEntity;
 
@@ -17,14 +18,17 @@
  * 
  */
 public class GroundhogDB {
-	private final String dbName;
-	private final MongoClient mongo;
-    private final Datastore datastore;
+
+	private String dbName;
+	private MongoClient mongo;
+    private Datastore datastore;
+    private Morphia mapper;
 
 	public GroundhogDB(String host, String dbName) throws UnknownHostException {
 		this.dbName = dbName;
 		this.mongo = new MongoClient(host);
-		this.datastore = new Morphia().createDatastore(this.mongo, dbName);
+		this.mapper = new Morphia();
+		this.datastore = this.mapper.createDatastore(this.mongo, dbName);
 	}
 
 	public GroundhogDB(MongoClient mongo, String dbName) throws UnknownHostException {
@@ -41,8 +45,8 @@ public static void query(GitHubEntity entity, String params) {
 	 * Receives a GitHub entity object and persists it to the database
 	 * @param entity, a {@link Object} representing one of the many GitHub entities covered by Groundhog
 	 */
-	public void save(Object entity) {
-		this.datastore.save(entity);
+	public <T> Key<T> save(T entity) {
+		return this.datastore.save(entity);
 	}
 
 	public String getDbName() {
@@ -56,4 +60,17 @@ public MongoClient getMongo() {
 	public Datastore getDatastore() {
 		return this.datastore;
 	}
-}
+
+	public void setDatastore(Datastore datastore) {
+		this.datastore = datastore;
+	}
+
+	public Morphia getMapper() {
+		return mapper;
+	}
+
+	public void setMapper(Morphia mapper) {
+		this.mapper = mapper;
+	}
+
+}

src/java/main/br/ufpe/cin/groundhog/extractor/GitCommitExtractor.java

@@ -41,6 +41,21 @@ public List<Commit> extractCommits(File project) {
 		return null;
 	}
 
+	public List<RevCommit> getCommitList(File project) {
+		CommitListFilter list = new CommitListFilter();
+
+		String path = project.getAbsolutePath() + "/.git";
+		CommitFinder finder = new CommitFinder(path);
+
+		finder.setFilter(list).find();
+//		
+//		for (RevCommit rev : list.getCommits()){
+//		    System.out.println(rev.getName() + " " + rev.getAuthorIdent().getName() + " " + rev.getShortMessage());
+//		}
+//		
+		return list.getCommits();
+	}
+
 	/**
 	 * A method that returns the number of commits that contain files with a given file extension
 	 * Example usage:

src/java/main/br/ufpe/cin/groundhog/main/CmdMain.java

@@ -3,6 +3,7 @@
 import static java.lang.String.format;
 
 import java.io.File;
+import java.net.UnknownHostException;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.HashMap;
@@ -28,8 +29,14 @@
 import br.ufpe.cin.groundhog.crawler.CrawlGoogleCode;
 import br.ufpe.cin.groundhog.crawler.CrawlSourceForge;
 import br.ufpe.cin.groundhog.crawler.ForgeCrawler;
+import br.ufpe.cin.groundhog.database.GroundhogDB;
 import br.ufpe.cin.groundhog.http.HttpModule;
 import br.ufpe.cin.groundhog.http.Requests;
+import br.ufpe.cin.groundhog.metrics.JavaProject;
+import br.ufpe.cin.groundhog.metrics.exception.InvalidJavaFileException;
+import br.ufpe.cin.groundhog.metrics.exception.InvalidJavaProjectPathException;
+import br.ufpe.cin.groundhog.metrics.exception.InvalidSourceRootCodePathException;
+import br.ufpe.cin.groundhog.metrics.exception.InvalidTestSourcePathException;
 import br.ufpe.cin.groundhog.parser.java.JavaParser;
 import br.ufpe.cin.groundhog.parser.java.MutableInt;
 import br.ufpe.cin.groundhog.parser.java.NotAJavaProjectException;
@@ -171,7 +178,7 @@ public File downloadAndCheckoutProject(Project project,
 
 			File repositoryFolder = repositoryFolderFuture.get();
 			logger.info(format("Project %s was downloaded", name));
-			
+
 			logger.info(format("Project has %d forks", project.getForksCount()));
 
 			logger.info(format("Checking out project %s to %s...", name, datetimeStr));
@@ -237,74 +244,99 @@ public void analyzeProject(Project project, File projectFolder,
 	@Override
 	public void run(JsonInputFile input) {
 		try {
-			final File destinationFolder = input.getDest();
-			final File metricsFolder = input.getOut();
-
-			logger.info("Creating temp folders...");
-			createTempFolders(destinationFolder, metricsFolder);
-
-			final Date datetime = input.getDatetime();
-			final int nProjects = input.getNprojects();
-			final String username = input.getSearch().getUsername();
-
-			// Search for projects
-			logger.info("Searching for projects... " + input.getSearch().getProjects());
-			ForgeSearch search = defineForgeSearch(input.getForge());
-			ForgeCrawler crawler = defineForgeCrawler(input.getForge(), destinationFolder);
-
-			String term = input.getSearch().getProjects().get(0);
 
-			List<Project> allProjects = null;
-			if(username != null && !username.isEmpty()) {
-				allProjects = search.getProjects(term, username, 1);				
-			} else {
-				allProjects = search.getProjects(term, 1,-1);
-			}
-
-			//TODO the getProjects method already limits the number of searched projects
-			List<Project> projects = new ArrayList<Project>();
-			for (int i = 0; i < nProjects; i++) {
-				if (i < allProjects.size()) {
-					projects.add(allProjects.get(i));
+			//Java Metrics
+			if(input.getDBName()!= null || input.getJavaProjectSourceRootPath() != null || input.getJavaProjectSourceRootTestPath() != null){
+
+				final GroundhogDB ghdb = new GroundhogDB("127.0.0.1", input.getDBName());
+				ghdb.getMapper().mapPackage("br.ufpe.cin.groundhog.metrics");
+
+				JavaProject project = new JavaProject(input.getJavaProjectPath());
+				try {
+					project.generateStructure(input.getJavaProjectSourceRootPath(), input.getJavaProjectSourceRootTestPath());
+				} catch (Exception e) {
+					logger.error("The struture of passed Java project can't be reconstructed!\nPlease check your parameters");
+					e.printStackTrace();
+				}
+
+				project.generateMetrics(
+						input.getJavaProjectSourceRootTestPath() != null ? true: false,
+								ghdb);
+
+			}else{
+
+				final File destinationFolder = input.getDest();
+				final File metricsFolder = input.getOut();
+
+				logger.info("Creating temp folders...");
+				createTempFolders(destinationFolder, metricsFolder);
+
+				final Date datetime = input.getDatetime();
+				final int nProjects = input.getNprojects();
+				final String username = input.getSearch().getUsername();
+
+				// Search for projects
+				logger.info("Searching for projects... " + input.getSearch().getProjects());
+				ForgeSearch search = defineForgeSearch(input.getForge());
+				ForgeCrawler crawler = defineForgeCrawler(input.getForge(), destinationFolder);
+
+				String term = input.getSearch().getProjects().get(0);
+
+				List<Project> allProjects = null;
+				if(username != null && !username.isEmpty()) {
+					allProjects = search.getProjects(term, username, 1);				
+				} else {
+					allProjects = search.getProjects(term, 1,-1);
 				}
-			}
-
-			// Download and analyze projects
-			logger.info("Downloading and processing projects...");
-			ExecutorService ex = Executors.newFixedThreadPool(JsonInputFile.getMaxThreads());
-			List<Future<File>> downloadFutures = crawler.asyncDownloadProjects(projects);
-			List<Future<?>> analysisFutures = new ArrayList<Future<?>>();
-
-			for (int i = 0; i < downloadFutures.size(); i++) {
-				final Project project = projects.get(i);
-				final Future<File> repositoryFolderFuture = downloadFutures.get(i);
-				final Formater metricsFormat = input.getOutputformat();
 
-				analysisFutures.add(ex.submit(new Runnable() {
-					@Override
-					public void run() {
-						File checkedOutRepository = downloadAndCheckoutProject(project, datetime, repositoryFolderFuture);
+				//TODO the getProjects method already limits the number of searched projects
+				List<Project> projects = new ArrayList<Project>();
+				for (int i = 0; i < nProjects; i++) {
+					if (i < allProjects.size()) {
+						projects.add(allProjects.get(i));
+					}
+				}
 
-						if (checkedOutRepository != null) {
-							analyzeProject(project, checkedOutRepository, datetime, metricsFolder, metricsFormat);
+				// Download and analyze projects
+				logger.info("Downloading and processing projects...");
+				ExecutorService ex = Executors.newFixedThreadPool(JsonInputFile.getMaxThreads());
+				List<Future<File>> downloadFutures = crawler.asyncDownloadProjects(projects);
+				List<Future<?>> analysisFutures = new ArrayList<Future<?>>();
+
+				for (int i = 0; i < downloadFutures.size(); i++) {
+					final Project project = projects.get(i);
+					final Future<File> repositoryFolderFuture = downloadFutures.get(i);
+					final Formater metricsFormat = input.getOutputformat();
+
+					analysisFutures.add(ex.submit(new Runnable() {
+						@Override
+						public void run() {
+							File checkedOutRepository = downloadAndCheckoutProject(project, datetime, repositoryFolderFuture);
+
+							if (checkedOutRepository != null) {
+								analyzeProject(project, checkedOutRepository, datetime, metricsFolder, metricsFormat);
+							}
 						}
-					}
-				}));
-			}
+					}));
+				}
 
-			ex.shutdown();
-			for (int i = 0; i < analysisFutures.size(); i++) {
-				try {
-					analysisFutures.get(i).get();
-				} catch (InterruptedException | ExecutionException e) {
-					logger.error(format("Error while analyzing project %s", projects.get(i).getName()), e);
+				ex.shutdown();
+				for (int i = 0; i < analysisFutures.size(); i++) {
+					try {
+						analysisFutures.get(i).get();
+					} catch (InterruptedException | ExecutionException e) {
+						logger.error(format("Error while analyzing project %s", projects.get(i).getName()), e);
+					}
 				}
+				logger.info("All projects were downloaded and analyzed!");
 			}
-			logger.info("All projects were downloaded and analyzed!");
-
+
 		} catch (GroundhogException e) {
 			e.printStackTrace();
 			logger.error(e.getMessage());
+		} catch (UnknownHostException e1) {
+			e1.printStackTrace();
+			logger.error("Fail to acess MongoDB database, please check if its installed and running");
 		}
 	}