refs 4896: SAI enhancements

Task-Url: https://support.d4science.org/issues/4896

Added manage versioning of the R packages

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/portlets/user/statistical-algorithms-importer@131256 82a268e6-3cf1-43bd-a215-b396298e98cf

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/client/tools/input/InputOutputVariablesPanel.java

@@ -268,6 +268,7 @@ public class InputOutputVariablesPanel extends ContentPanel {
 		TextField defaultValueColumnEditing = new TextField();
 		defaultValueColumnEditing.addValidator(new RegExValidator("^[^\"\\\\]*(?:\\\\.[^\"\\\\]*)*$",
 				"Attention character \" is not allowed"));
+		defaultValueColumnEditing.setAllowBlank(false);
 		
 		gridInputOutputVariablesEditing = new GridRowEditing<InputOutputVariables>(
 				gridInputOutputVariables);

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/server/SessionUtil.java

@@ -13,6 +13,7 @@ import javax.servlet.http.HttpSession;
 
 import org.gcube.application.framework.core.session.ASLSession;
 import org.gcube.application.framework.core.session.SessionManager;
+import org.gcube.common.authorization.library.provider.UserInfo;
 import org.gcube.portal.custom.scopemanager.scopehelper.ScopeHelper;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.server.file.CodeFileUploadSession;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.server.social.Recipient;
@@ -69,7 +70,8 @@ public class SessionUtil {
 		return aslSession;
 	}
 
-	public static String getToken(ASLSession aslSession) {
+	public static String getToken(ASLSession aslSession)
+			throws StatAlgoImporterServiceException {
 		String token = null;
 		if (Constants.DEBUG_MODE) {
 			List<String> userRoles = new ArrayList<>();
@@ -78,8 +80,17 @@ public class SessionUtil {
 			 * if (aslSession.getUsername().compareTo("lucio.lelii") == 0)
 			 * userRoles.add("VRE-Manager");
 			 */
-			token = authorizationService().build().generate(
+			try {
-					aslSession.getUsername(), userRoles);
+				token = authorizationService().generateUserToken(
+						new UserInfo(aslSession.getUsername(), userRoles),
+						aslSession.getScope());
+			} catch (Exception e) {
+				logger.error("Error generating the token for test: "
+						+ e.getLocalizedMessage());
+				e.printStackTrace();
+				throw new StatAlgoImporterServiceException("Error generating the token for test: "
+						+ e.getLocalizedMessage());
+			}
 
 		} else {
 			token = aslSession.getSecurityToken();
@@ -134,8 +145,7 @@ public class SessionUtil {
 
 	//
 	public static void setCodeFileUploadSession(HttpSession httpSession,
-			CodeFileUploadSession s)
+			CodeFileUploadSession s) throws StatAlgoImporterServiceException {
-			throws StatAlgoImporterServiceException {
 
 		CodeFileUploadSession session = (CodeFileUploadSession) httpSession
 				.getAttribute(SessionConstants.IMPORT_CODE_FILE_UPLOAD_SESSION);
@@ -144,7 +154,7 @@ public class SessionUtil {
 					.removeAttribute(SessionConstants.IMPORT_CODE_FILE_UPLOAD_SESSION);
 		httpSession.setAttribute(
 				SessionConstants.IMPORT_CODE_FILE_UPLOAD_SESSION, s);
-		
+
 	}
 
 	public static CodeFileUploadSession getCodeFileUploadSession(

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/server/generator/ProjectBuilder.java

@@ -9,7 +9,9 @@ import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.nio.file.StandardOpenOption;
+import java.text.SimpleDateFormat;
 import java.util.ArrayList;
+import java.util.GregorianCalendar;
 import java.util.List;
 
 import org.apache.commons.io.FileUtils;
@@ -40,7 +42,10 @@ public class ProjectBuilder {
 	private static final String STATISTICAL_ALGORITHM_DEPLOY_FOLDER_DESCRIPTION = "Project Deploy";
 	private static final String STATISTICAL_ALGORITHM_COMPILE_FOLDER_NAME = "Compile";
 	private static final String STATISTICAL_ALGORITHM_COMPILE_FOLDER_DESCRIPTION = "Project Compile";
-
+	private static final String STATISTICAL_ALGORITHM_BACKUP_FOLDER_NAME = "Backup";
+	private static final String STATISTICAL_ALGORITHM_BACKUP_FOLDER_DESCRIPTION = "Project Backup";
+	
+	
 	private static final String ALGORITHM_MIMETYPE = "text/plain";
 	private static final String ALGORITHM_DESCRIPTION = "Statistical Algorithm Java Code";
 	private static final String ALGORITHM_EXTENTION = ".java";
@@ -62,13 +67,18 @@ public class ProjectBuilder {
 	private static final String CODE_JAR_DESCRIPTION = "Statistical Algorithm Jar";
 	private static final String JAR_EXTENTION = ".jar";
 
+	private static final SimpleDateFormat sdf = new SimpleDateFormat(
+			"yyyyMMdd_HHmmss");
+
 	public static final Logger logger = LoggerFactory
 			.getLogger(ProjectBuilder.class);
 
 	private Project project;
+	private String backupFolderId;
 	private ASLSession aslSession;
 	private Path algorithmJava;
 	private Path infoTXT;
+	
 
 	public ProjectBuilder(Project project, ASLSession aslSession) {
 		this.project = project;
@@ -77,6 +87,7 @@ public class ProjectBuilder {
 
 	public Project buildTarget() throws StatAlgoImporterServiceException {
 		checkInfoForBuild();
+		createBackup();
 		createTargetFolder();
 		createDeployFolder();
 		createProjectPackage();
@@ -102,6 +113,7 @@ public class ProjectBuilder {
 
 	}
 
+
 	public Project buildDeploy() throws StatAlgoImporterServiceException {
 		checkInfoForDeploy();
 		copyJarInDeploy();
@@ -110,15 +122,25 @@ public class ProjectBuilder {
 
 	public Project buildRepackage() throws StatAlgoImporterServiceException {
 		checkInfoForRepackage();
+		createBackupOfPackageProject();
 		repackageProjectPackage();
 		return project;
 	}
 
+	private void createBackup() throws StatAlgoImporterServiceException {
+		createBackupOfPackageProject();
+	}
+	
+	
 	private void repackageProjectPackage()
 			throws StatAlgoImporterServiceException {
+		List<String> idsToExclude = new ArrayList<String>();
+		idsToExclude.add(backupFolderId);
+		
+		
 		FilesStorage filesStorage = new FilesStorage();
 
-		List<String> idsToExclude = new ArrayList<String>();
+		
 		if (project.getProjectTarget() != null
 				&& project.getProjectTarget().getFolder() != null
 				&& project.getProjectTarget().getFolder().getId() != null
@@ -157,7 +179,7 @@ public class ProjectBuilder {
 					packageProject.getOwner().getPortalLogin(),
 					packageProject.getPath(), packageProject.getType().name());
 			packageProjectItemDescription.setPublicLink(packageProject
-					.getPublicLink(true));
+					.getPublicLink(false));
 		} catch (InternalErrorException e) {
 			logger.error(e.getLocalizedMessage());
 			e.printStackTrace();
@@ -172,6 +194,37 @@ public class ProjectBuilder {
 
 	}
 
+	private void createBackupOfPackageProject()
+			throws StatAlgoImporterServiceException {
+		logger.debug("Create Backup of PackageProject");
+		if (project.getProjectTarget() != null
+				&& project.getProjectTarget().getProjectDeploy() != null
+				&& project.getProjectTarget().getProjectDeploy()
+						.getPackageProject() != null
+				&& project.getProjectTarget().getProjectDeploy()
+						.getPackageProject().getId() != null
+				&& !project.getProjectTarget().getProjectDeploy()
+						.getPackageProject().getId().isEmpty()) {
+			
+			createBackupFolder();
+			
+			FilesStorage filesStorage = new FilesStorage();
+
+			GregorianCalendar now = new GregorianCalendar();
+
+			String packageProjectNewName = project.getInputData()
+					.getProjectInfo().getAlgorithmNameToClassName()
+					+ "_backup_"
+					+ sdf.format(now.getTime())
+					+ PROJECT_PACKAGE_EXTENTION;
+
+			filesStorage.copyItemOnFolderWithNewName(aslSession.getUsername(),
+					project.getProjectTarget().getProjectDeploy()
+							.getPackageProject().getId(), backupFolderId, packageProjectNewName);
+		}
+
+	}
+
 	private void copyJarInDeploy() throws StatAlgoImporterServiceException {
 		FilesStorage filesStorage = new FilesStorage();
 		if (project.getProjectTarget().getProjectDeploy().getCodeJar() != null
@@ -200,7 +253,7 @@ public class ProjectBuilder {
 							.getOwner().getPortalLogin(),
 					deployableCodeJarItem.getPath(), deployableCodeJarItem
 							.getType().name());
-			dCodeJar.setPublicLink(deployableCodeJarItem.getPublicLink(true));
+			dCodeJar.setPublicLink(deployableCodeJarItem.getPublicLink(false));
 		} catch (InternalErrorException e) {
 			logger.error(e.getLocalizedMessage());
 			e.printStackTrace();
@@ -409,9 +462,12 @@ public class ProjectBuilder {
 	}
 
 	private void createProjectPackage() throws StatAlgoImporterServiceException {
+		List<String> idsToExclude = new ArrayList<String>();
+		idsToExclude.add(backupFolderId);
+		
 		FilesStorage filesStorage = new FilesStorage();
 
-		List<String> idsToExclude = new ArrayList<String>();
+		
 		if (project.getProjectTarget() != null
 				&& project.getProjectTarget().getFolder() != null
 				&& project.getProjectTarget().getFolder().getId() != null
@@ -452,7 +508,7 @@ public class ProjectBuilder {
 					projectPackageItem.getName(), projectPackageItem.getOwner()
 							.getPortalLogin(), projectPackageItem.getPath(),
 					projectPackageItem.getType().name());
-			packageUrl.setPublicLink(projectPackageItem.getPublicLink(true));
+			packageUrl.setPublicLink(projectPackageItem.getPublicLink(false));
 		} catch (InternalErrorException e) {
 			logger.error(e.getLocalizedMessage());
 			e.printStackTrace();
@@ -523,6 +579,43 @@ public class ProjectBuilder {
 		project.getProjectTarget().setProjectCompile(projectCompile);
 	}
 
+	private void createBackupFolder() throws StatAlgoImporterServiceException {
+		FilesStorage filesStorage = new FilesStorage();
+		
+		WorkspaceItem backupFolder=filesStorage.find(aslSession.getUsername(), project
+				.getProjectFolder().getFolder().getId(), STATISTICAL_ALGORITHM_BACKUP_FOLDER_NAME);
+		
+		if(backupFolder==null){
+			WorkspaceFolder newBackupFolder = filesStorage.createFolder(
+					aslSession.getUsername(), project.getProjectFolder()
+							.getFolder().getId(),
+					STATISTICAL_ALGORITHM_BACKUP_FOLDER_NAME,
+					STATISTICAL_ALGORITHM_BACKUP_FOLDER_DESCRIPTION);
+			logger.debug("BackupFolder:" + backupFolder);
+			
+			try {
+				backupFolderId=newBackupFolder.getId();
+			} catch (InternalErrorException e) {
+				logger.error("Error retrieving Backup Folder Id: "+e.getLocalizedMessage());
+				e.printStackTrace();
+				throw new StatAlgoImporterServiceException("Error retrieving Backup Folder Id",e);
+			}
+			
+		} else {
+			try {
+				backupFolderId=backupFolder.getId();
+			} catch (InternalErrorException e) {
+				logger.error("Error retrieving Backup Folder Id: "+e.getLocalizedMessage());
+				e.printStackTrace();
+				throw new StatAlgoImporterServiceException("Error retrieving Backup Folder Id",e);
+			}
+		}
+		
+		
+		
+	}
+	
+	
 	private void createAlgorithm() throws StatAlgoImporterServiceException {
 		AlgorithmGenerator algorithmGenerator = new AlgorithmGenerator(project);
 		algorithmJava = algorithmGenerator.createAlgorithm();
@@ -551,7 +644,7 @@ public class ProjectBuilder {
 					algorithmItem.getName(), algorithmItem.getOwner()
 							.getPortalLogin(), algorithmItem.getPath(),
 					algorithmItem.getType().name());
-			codeSource.setPublicLink(algorithmItem.getPublicLink(true));
+			codeSource.setPublicLink(algorithmItem.getPublicLink(false));
 		} catch (InternalErrorException e) {
 			logger.error(e.getLocalizedMessage());
 			e.printStackTrace();
@@ -594,7 +687,7 @@ public class ProjectBuilder {
 					infoItem.getName(), infoItem.getOwner().getPortalLogin(),
 					infoItem.getPath(), infoItem.getType().name());
 			integrationItemDescription.setPublicLink(infoItem
-					.getPublicLink(true));
+					.getPublicLink(false));
 		} catch (InternalErrorException e) {
 			logger.error(e.getLocalizedMessage());
 			e.printStackTrace();
@@ -729,7 +822,7 @@ public class ProjectBuilder {
 							.getPortalLogin(), codeJarItem.getPath(),
 					codeJarItem.getType().name());
 			codeJarItemDescription.setPublicLink(codeJarItem
-					.getPublicLink(true));
+					.getPublicLink(false));
 		} catch (InternalErrorException e) {
 			logger.error(e.getLocalizedMessage());
 			e.printStackTrace();
@@ -749,9 +842,9 @@ public class ProjectBuilder {
 
 		try {
 
-			ProcessBuilder pb = new ProcessBuilder("javac", "-encoding", "utf-8","-cp",
+			ProcessBuilder pb = new ProcessBuilder("javac", "-encoding",
-					tempDirectory.toAbsolutePath().toString() + "/*",
+					"utf-8", "-cp", tempDirectory.toAbsolutePath().toString()
-					packageHome.toAbsolutePath().toString()
+							+ "/*", packageHome.toAbsolutePath().toString()
 							+ File.separator
 							+ project.getInputData().getProjectInfo()
 									.getAlgorithmNameToClassName()

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/server/storage/FilesStorage.java

@@ -117,6 +117,49 @@ public class FilesStorage {
 		}
 	}
 
+	/**
+	 * 
+	 * @param user
+	 *            User
+	 * @param itemId
+	 *            Item id
+	 * @param folderId
+	 *            Destination folder id
+	 * @param newName
+	 *            New name
+	 * 
+	 * @throws StatAlgoImporterServiceException
+	 */
+	public WorkspaceItem copyItemOnFolderWithNewName(String user,
+			String itemId, String folderId, String newName)
+			throws StatAlgoImporterServiceException {
+		Workspace ws;
+		try {
+			ws = HomeLibrary.getUserWorkspace(user);
+
+			WorkspaceItem workSpaceItem = ws.getItem(folderId);
+			if (!workSpaceItem.isFolder()) {
+				throw new StatAlgoImporterServiceException(
+						"Destination is not a folder!");
+			}
+
+			WorkspaceItem item = ws.copy(itemId, newName, folderId);
+
+			return item;
+		} catch (WrongDestinationException | ItemAlreadyExistException
+				| InsufficientPrivilegesException
+				| WorkspaceFolderNotFoundException | InternalErrorException
+				| HomeNotFoundException | ItemNotFoundException e) {
+			e.printStackTrace();
+			throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
+
+		}
+	}
+	
+	
+	
+	
+
 	/**
 	 * 
 	 * @param user
@@ -218,6 +261,39 @@ public class FilesStorage {
 
 	}
 
+	/**
+	 * 
+	 * @param user
+	 *            User
+	 * @param parentId
+	 *            Destination folder id
+	 * @return Folder
+	 * @throws StatAlgoImporterServiceException
+	 */
+	public WorkspaceItem find(String user, String parentId, String name)
+			throws StatAlgoImporterServiceException {
+		Workspace ws;
+		try {
+			ws = HomeLibrary.getUserWorkspace(user);
+
+			WorkspaceItem workSpaceItem = ws.getItem(parentId);
+			if (!workSpaceItem.isFolder()) {
+				throw new StatAlgoImporterServiceException(
+						"No valid project folder!");
+			}
+
+			return ws.find(name, parentId);
+			
+		} catch (WorkspaceFolderNotFoundException | InternalErrorException
+				| HomeNotFoundException | ItemNotFoundException
+				| WrongItemTypeException e) {
+			e.printStackTrace();
+			throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
+
+		}
+
+	}
+
 	/**
 	 * 
 	 * @param user
@@ -503,7 +579,7 @@ public class FilesStorage {
 			org.gcube.common.homelibrary.home.workspace.folder.items.File gcubeItem = ((org.gcube.common.homelibrary.home.workspace.folder.items.File) wi);
 			is = gcubeItem.getData();
 			return is;
-		
+
 		} catch (Throwable e) {
 			logger.error("Error retrieving file from storage", e);
 			e.printStackTrace();