1452: Implement a GUI for StatMan Algorithms Importer

Task-Url: https://support.d4science.org/issues/1452

File jar now include package folder

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/portlets/user/statistical-algorithms-importer@122439 82a268e6-3cf1-43bd-a215-b396298e98cf

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/client/tools/explorer/ExplorerProjectPanel.java

@@ -113,11 +113,13 @@ public class ExplorerProjectPanel extends ContentPanel {
 			break;
 		case OPEN:
 		case UPDATE:
-		case SAVE:
 		case ADD_RESOURCE:
 		case DELETE_RESOURCE:
 			create(event);
 			break;
+		case SAVE:	
+			reloadWSResourceExplorerPanel();
+			break;
 		case MAIN_CODE_SET:
 			reloadWSResourceExplorerPanel();
 			break;

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

@@ -68,7 +68,7 @@ public class InfoGenerator {
 							+ project.getInputData().getProjectInfo()
 									.getAlgorithmNameToUpper());
 					infos.add("Class Name: org.gcube.dataanalysis.executor.rscripts."+ project.getInputData().getProjectInfo()
-							.getAlgorithmNameToUpper());
+							.getAlgorithmNameToClassName());
 				
 				} else {
 					infos.add("Algorithm Name: ");

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

@@ -4,7 +4,6 @@ import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
 import java.lang.ProcessBuilder.Redirect;
-import java.nio.file.DirectoryStream;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
@@ -302,43 +301,90 @@ public class ProjectBuilder {
 	}
 
 	private void createProjectJarFile() throws StatAlgoImporterServiceException {
+
+		FilesStorage storage = new FilesStorage();
+
+		Path tempDirectory;
 		try {
-			FilesStorage storage = new FilesStorage();
+			tempDirectory = Files.createTempDirectory("StatAlgorithmsJar");
-
-			Path tempDirectory = Files.createTempDirectory("StatAlgorithmsJar");
-			logger.debug("TempDir: " + tempDirectory);
-			Path ecologicalEngineJar = new File(tempDirectory.toFile(),
-					ECOLOGICAL_ENGINE_JAR).toPath();
-			storage.downloadInputFile(ECOLOGICAL_ENGINE_JAR_URL,
-					ecologicalEngineJar);
-			Path ecologicalEngineSmartExecutorJar = new File(
-					tempDirectory.toFile(),
-					ECOLOGICAL_ENGINE_SMART_EXECUTOR_JAR).toPath();
-			storage.downloadInputFile(ECOLOGICAL_ENGINE_SMART_EXECUTOR_JAR_URL,
-					ecologicalEngineSmartExecutorJar);
-			Path algorithmTempFile = new File(tempDirectory.toFile(), project
-					.getInputData().getProjectInfo()
-					.getAlgorithmNameToClassName()
-					+ ALGORITHM_EXTENTION).toPath();
-			Files.copy(algorithmJava, algorithmTempFile);
-			Path infoTempFile = new File(tempDirectory.toFile(), INFO_NAME
-					+ INFO_EXTENTION).toPath();
-			Files.copy(infoTXT, infoTempFile);
-
-			createClassFile(tempDirectory);
-			createJarFile(tempDirectory, infoTempFile);
-			copyJarOnWorkspace(tempDirectory);
-			FileUtils.cleanDirectory(tempDirectory.toFile());
-			FileUtils.deleteDirectory(tempDirectory.toFile());
-
-			return;
-
 		} catch (IOException e) {
-			logger.error(e.getLocalizedMessage());
+			logger.error("Error creating temporal directory: "
+					+ e.getLocalizedMessage());
 			e.printStackTrace();
 			throw new StatAlgoImporterServiceException(e.getLocalizedMessage(),
 					e);
 		}
+		logger.debug("TempDir: " + tempDirectory);
+
+		File packageHome = new File(tempDirectory.toAbsolutePath().toString()
+				+ File.separator + "org" + File.separator + "gcube"
+				+ File.separator + "dataanalysis" + File.separator + "executor"
+				+ File.separator + "rscripts");
+		packageHome.mkdirs();
+		Path packageHomeDir = packageHome.toPath();
+
+		Path ecologicalEngineJar = new File(tempDirectory.toFile(),
+				ECOLOGICAL_ENGINE_JAR).toPath();
+		storage.downloadInputFile(ECOLOGICAL_ENGINE_JAR_URL,
+				ecologicalEngineJar);
+		Path ecologicalEngineSmartExecutorJar = new File(
+				tempDirectory.toFile(), ECOLOGICAL_ENGINE_SMART_EXECUTOR_JAR)
+				.toPath();
+		storage.downloadInputFile(ECOLOGICAL_ENGINE_SMART_EXECUTOR_JAR_URL,
+				ecologicalEngineSmartExecutorJar);
+
+		Path algorithmTempFile = new File(packageHomeDir.toFile(), project
+				.getInputData().getProjectInfo().getAlgorithmNameToClassName()
+				+ ALGORITHM_EXTENTION).toPath();
+		try {
+			Files.copy(algorithmJava, algorithmTempFile);
+		} catch (IOException e) {
+			logger.error("Error in alogrithm java copy in package directory: "
+					+ e.getLocalizedMessage());
+			e.printStackTrace();
+			throw new StatAlgoImporterServiceException(e.getLocalizedMessage(),
+					e);
+		}
+
+		Path infoTempFile = new File(tempDirectory.toFile(), INFO_NAME
+				+ INFO_EXTENTION).toPath();
+		try {
+			Files.copy(infoTXT, infoTempFile);
+		} catch (IOException e) {
+			logger.error("Error in info copy in temp directory: "
+					+ e.getLocalizedMessage());
+			e.printStackTrace();
+			throw new StatAlgoImporterServiceException(e.getLocalizedMessage(),
+					e);
+		}
+
+		createClassFile(tempDirectory, packageHomeDir);
+
+		try {
+			Files.delete(algorithmTempFile);
+		} catch (IOException e) {
+			logger.error("Error in delete java file in package directory: "
+					+ e.getLocalizedMessage());
+			e.printStackTrace();
+			throw new StatAlgoImporterServiceException(e.getLocalizedMessage(),
+					e);
+		}
+
+		createJarFile(tempDirectory, infoTempFile);
+		copyJarOnWorkspace(tempDirectory);
+
+		try {
+			FileUtils.cleanDirectory(tempDirectory.toFile());
+			FileUtils.deleteDirectory(tempDirectory.toFile());
+		} catch (IOException e) {
+			logger.error("Error in delete temp directory: "
+					+ e.getLocalizedMessage());
+			e.printStackTrace();
+			throw new StatAlgoImporterServiceException(e.getLocalizedMessage(),
+					e);
+		}
+		return;
+
 	}
 
 	private void copyJarOnWorkspace(Path tempDirectory)
@@ -387,15 +433,17 @@ public class ProjectBuilder {
 
 	}
 
-	private void createClassFile(Path tempDirectory)
+	private void createClassFile(Path tempDirectory, Path packageHome)
 			throws StatAlgoImporterServiceException {
 
 		try {
 
 			ProcessBuilder pb = new ProcessBuilder("javac", "-cp",
-					tempDirectory.toAbsolutePath().toString() + "/*", project
+					tempDirectory.toAbsolutePath().toString() + "/*",
-							.getInputData().getProjectInfo()
+					packageHome.toAbsolutePath().toString()
-							.getAlgorithmNameToClassName()
+							+ File.separator
+							+ project.getInputData().getProjectInfo()
+									.getAlgorithmNameToClassName()
 							+ ALGORITHM_EXTENTION);
 			pb.directory(tempDirectory.toFile());
 			Path logTXT = new File(tempDirectory.toFile(), LOG_TXT).toPath();
@@ -428,14 +476,16 @@ public class ProjectBuilder {
 					.getAlgorithmNameToClassName()
 					+ JAR_EXTENTION);
 
-			DirectoryStream<Path> directoryStream = Files
+			/*
-					.newDirectoryStream(tempDirectory);
+			 * DirectoryStream<Path> directoryStream = Files
-			for (Path path : directoryStream) {
+			 * .newDirectoryStream(tempDirectory); for (Path path :
-				if (path.toString().endsWith(".class"))
+			 * directoryStream) { if (path.toString().endsWith(".class"))
-					commands.add(path.getFileName().toString());
+			 * commands.add(path.getFileName().toString());
-
+			 * 
-			}
+			 * }
+			 */
 
+			commands.add("org");
 			commands.add(infoTempFile.getFileName().toString());
 
 			ProcessBuilder pb = new ProcessBuilder(commands);