ref 8819: Extend The Algorithms Importer to Manage Many Processes as Black Boxes

https://support.d4science.org/issues/8819

Updated the support for Processes as Black Boxes

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/portlets/user/statistical-algorithms-importer@150968 82a268e6-3cf1-43bd-a215-b396298e98cf

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/client/StatAlgoImporterController.java

@@ -462,7 +462,7 @@ public class StatAlgoImporterController {
 
 	private void doSetNewMainCodeEvent(NewCodeEvent event) {
 		monitor = new StatAlgoImporterMonitor();
-		pm.setNewMainCode(event, monitor);
+		pm.setNewCode(event, monitor);
 
 	}
 

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/client/maindata/CodeEditPanel.java

@@ -326,10 +326,7 @@ public class CodeEditPanel extends ContentPanel {
 					}
 
 				} else {
-					editor.setShowPrintMargin(false);
+					
-					editor.setMode(AceEditorMode.R);
-					editor.setTheme(AceEditorTheme.ECLIPSE);
-					editor.setText("");
 				}
 
 				if (project != null) {

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/client/project/ProjectManager.java

@@ -522,8 +522,8 @@ public class ProjectManager {
 
 	}
 
-	public void setNewMainCode(NewCodeEvent newMainCodeEvent, final StatAlgoImporterMonitor monitor) {
+	public void setNewCode(NewCodeEvent newCodeEvent, final StatAlgoImporterMonitor monitor) {
-		StatAlgoImporterServiceAsync.INSTANCE.setNewCode(newMainCodeEvent.getFile(), newMainCodeEvent.getCode(),
+		StatAlgoImporterServiceAsync.INSTANCE.setNewCode(newCodeEvent.getFile(), newCodeEvent.getCode(),
 				new AsyncCallback<Project>() {
 
 					@Override
@@ -532,7 +532,7 @@ public class ProjectManager {
 						if (caught instanceof StatAlgoImporterSessionExpiredException) {
 							eventBus.fireEvent(new SessionExpiredEvent(SessionExpiredType.EXPIREDONSERVER));
 						} else {
-							Log.error("Error on save new main code: " + caught.getLocalizedMessage());
+							Log.error("Error on save new code: " + caught.getLocalizedMessage());
 							UtilsGXT3.alert("Error", caught.getLocalizedMessage());
 						}
 						caught.printStackTrace();
@@ -548,6 +548,10 @@ public class ProjectManager {
 
 				});
 	}
+	
+	
+	
+	
 
 	public void setBinaryCode(final InputData inputData,final ItemDescription itemDescription) {
 		if (project != null) {

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

@@ -17,7 +17,7 @@ import org.gcube.portlets.user.statisticalalgorithmsimporter.server.is.BuildSAID
 import org.gcube.portlets.user.statisticalalgorithmsimporter.server.social.AlgorithmNotification;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.server.social.Recipient;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.server.storage.FilesStorage;
-import org.gcube.portlets.user.statisticalalgorithmsimporter.server.storage.MainCodeSave;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.server.storage.CodeSave;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.server.storage.ProjectArchiver;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.server.util.ServiceCredentials;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.code.CodeData;
@@ -543,7 +543,7 @@ public class StatAlgoImporterServiceImpl extends RemoteServiceServlet implements
 						if (mainCode == null || mainCode.getItemDescription() == null) {
 							throw new StatAlgoImporterServiceException("No main code set!");
 						} else {
-							MainCodeSave mainCodeSave = new MainCodeSave();
+							CodeSave mainCodeSave = new CodeSave();
 							mainCodeSave.save(serviceCredentials, mainCode.getItemDescription(), code);
 						}
 					} else {
@@ -553,7 +553,7 @@ public class StatAlgoImporterServiceImpl extends RemoteServiceServlet implements
 							if (projectSupportBashEdit == null || projectSupportBashEdit.getBinaryItem() == null) {
 								throw new StatAlgoImporterServiceException("No binary code set!");
 							} else {
-								MainCodeSave mainCodeSave = new MainCodeSave();
+								CodeSave mainCodeSave = new CodeSave();
 								mainCodeSave.save(serviceCredentials, projectSupportBashEdit.getBinaryItem(), code);
 							}
 
@@ -588,15 +588,15 @@ public class StatAlgoImporterServiceImpl extends RemoteServiceServlet implements
 		try {
 			HttpServletRequest httpRequest = this.getThreadLocalRequest();
 			ServiceCredentials serviceCredentials = SessionUtil.getServiceCredentials(httpRequest);
-			logger.debug("saveCode(): itemDescription" + fileDescription + ", code:" + code);
+			logger.debug("saveNewCode(): itemDescription" + fileDescription + ", code:" + code);
 			Project project = SessionUtil.getProjectSession(httpRequest, serviceCredentials);
 			if (project != null && project.getProjectFolder() != null
 					&& project.getProjectFolder().getFolder() != null) {
 				if (project.getProjectConfig() != null && project.getProjectConfig().getProjectSupport() != null) {
 					if (project.getProjectConfig().getProjectSupport() instanceof ProjectSupportREdit) {
 
-						MainCodeSave mainCodeSave = new MainCodeSave();
+						CodeSave codeSave = new CodeSave();
-						ItemDescription mainCodeItemDescription = mainCodeSave.saveNew(serviceCredentials,
+						ItemDescription mainCodeItemDescription = codeSave.saveNew(serviceCredentials,
 								fileDescription, code, project.getProjectFolder().getFolder().getId());
 						MainCode mainCode = new MainCode(mainCodeItemDescription);
 						project.setMainCode(mainCode);
@@ -609,8 +609,8 @@ public class StatAlgoImporterServiceImpl extends RemoteServiceServlet implements
 							ProjectSupportBashEdit projectSupportBashEdit = (ProjectSupportBashEdit) project
 									.getProjectConfig().getProjectSupport();
 							
-							MainCodeSave mainCodeSave = new MainCodeSave();
+							CodeSave codeSave = new CodeSave();
-							ItemDescription binaryCodeItemDescription = mainCodeSave.saveNew(serviceCredentials,
+							ItemDescription binaryCodeItemDescription = codeSave.saveNew(serviceCredentials,
 									fileDescription, code, project.getProjectFolder().getFolder().getId());
 							projectSupportBashEdit.setBinaryItem(binaryCodeItemDescription);
 							project.setProjectTarget(null);

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/server/blackbox/GeneralPurposeScriptProducer.java

@@ -21,8 +21,7 @@ public class GeneralPurposeScriptProducer {
 	
 	private static final Logger logger = LoggerFactory.getLogger(GeneralPurposeScriptProducer.class);
 	public static final String REMOTE_TEMPLATE_FILE = "http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/data-analysis/RConfiguration/RD4SFunctions/SAITemplateForExternalInvocation.R";
-	public static final String PRE_INSTALLED = "Pre-Installed";
+	
-
 	
 	// name,type,default
 	public class Triple {
@@ -61,7 +60,7 @@ public class GeneralPurposeScriptProducer {
 			String URLtoSoftware) throws Exception {
 
 		String mainSoftwareName = mainSoftware;
-		if (softwareType.equals(PRE_INSTALLED)) {
+		if (URLtoSoftware!=null) {
 			mainSoftwareName = URLReader(URLtoSoftware);
 		}
 

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/server/blackbox/MainGenerator.java

@@ -76,7 +76,7 @@ public class MainGenerator {
 
 			Path producedScript = null;
 
-			if (project.getProjectConfig().getLanguage().compareTo(GeneralPurposeScriptProducer.PRE_INSTALLED) == 0) {
+			if (project.getProjectConfig().getProjectSupport() instanceof ProjectSupportBashEdit){
 				producedScript = s.generateScript(input, output, binarySoftware.getName(),
 						project.getProjectConfig().getLanguage(), binarySoftware.getPublicLink());
 			} else {

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

@@ -23,7 +23,7 @@ import org.slf4j.LoggerFactory;
  */
 public class InfoGenerator {
 	private static final String INFO_NAME = "Info";
-	private static final String INFO_EXTENTION = ".txt";
+	private static final String INFO_TXT_EXTENTION = ".txt";
 	public static final Logger logger = LoggerFactory.getLogger(InfoGenerator.class);
 
 	private Project project;
@@ -43,9 +43,9 @@ public class InfoGenerator {
 	public Path createInfo() throws StatAlgoImporterServiceException {
 
 		try {
-			Path tempFile = Files.createTempFile(INFO_NAME, INFO_EXTENTION);
+			Path tempFile = Files.createTempFile(INFO_NAME, INFO_TXT_EXTENTION);
 
-			List<String> lines = createInfoData();
+			List<String> lines = createInfoTxtData();
 			Files.write(tempFile, lines, Charset.defaultCharset(), StandardOpenOption.WRITE);
 			logger.debug(tempFile.toString());
 			return tempFile;
@@ -58,7 +58,7 @@ public class InfoGenerator {
 
 	}
 
-	private List<String> createInfoData() {
+	private List<String> createInfoTxtData() {
 		ArrayList<String> infos = new ArrayList<String>();
 		if (serviceCredentials != null) {
 			if (serviceCredentials.getUserName() != null && !serviceCredentials.getUserName().isEmpty()) {
@@ -84,8 +84,8 @@ public class InfoGenerator {
 		}
 		infos.add("");
 
-		if (project.getProjectConfig()!=null) {
+		if (project.getProjectConfig() != null) {
-			if(project.getProjectConfig().getLanguage()!=null){
+			if (project.getProjectConfig().getLanguage() != null) {
 				infos.add("Language: " + project.getProjectConfig().getLanguage());
 			} else {
 				infos.add("Language: ");
@@ -94,7 +94,6 @@ public class InfoGenerator {
 			infos.add("Language: ");
 		}
 
-		
 		if (project.getInputData() != null) {
 			if (project.getInputData().getProjectInfo() != null) {
 				if (project.getInputData().getProjectInfo().getAlgorithmName() != null) {
@@ -156,4 +155,5 @@ public class InfoGenerator {
 
 		return infos;
 	}
+
 }

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/server/is/BuildSAIDescriptor.java

@@ -25,6 +25,7 @@ public class BuildSAIDescriptor {
 		SAIDescriptor saiDescriptor = null;
 
 		if (Constants.DEBUG_MODE) {
+			logger.info("Debug Mode");
 			ArrayList<ProjectSetup> availableProjectConfigurations = new ArrayList<>();
 			ProjectSetup r = new ProjectSetup(ProjectLanguageType.R.getId(), ProjectSupportType.REDIT);
 			availableProjectConfigurations.add(r);
@@ -46,6 +47,7 @@ public class BuildSAIDescriptor {
 			availableProjectConfigurations.add(preInstalled);
 			saiDescriptor = new SAIDescriptor(availableProjectConfigurations);
 		} else {
+			logger.info("Production Mode");
 			SAIDescriptorJAXB saiDescriptorJAXB = null;
 			try {
 				saiDescriptorJAXB = InformationSystemUtils.retrieveSAIDescriptor(scope);
@@ -62,7 +64,7 @@ public class BuildSAIDescriptor {
 
 				for (AvailableProjectConfigJAXB availableProjectConfigJAXB : saiDescriptorJAXB
 						.getAvailableprojectconfiguration()) {
-					type = ProjectSupportType.valueOf(availableProjectConfigJAXB.getSupport());
+					type = ProjectSupportType.valueFromLabel(availableProjectConfigJAXB.getSupport());
 					if (type != null) {
 						availableProjectConfigurations
 								.add(new ProjectSetup(availableProjectConfigJAXB.getLanguage(), type));
@@ -70,6 +72,7 @@ public class BuildSAIDescriptor {
 					}
 				}
 			} else {
+				logger.info("Production Mode Default");
 				logger.info("SAIDescriptorJAXB use default configuration for scope: " + scope);
 
 				ProjectSetup r = new ProjectSetup(ProjectLanguageType.R.getId(), ProjectSupportType.REDIT);

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

@@ -19,53 +19,27 @@ import org.slf4j.LoggerFactory;
  * 
  *
  */
-public class MainCodeSave {
+public class CodeSave {
 	private static final String ALGORITHM_DESCRIPTION = "Algorithm";
 	private static final String ALGORITHM_MIMETYPE = "text/plain";
 
-	public static final Logger logger = LoggerFactory.getLogger(MainCodeSave.class);
+	public static final Logger logger = LoggerFactory.getLogger(CodeSave.class);
 
-	public MainCodeSave() {
+	public CodeSave() {
 
 	}
 
-	/**
-	 * 
-	 * @param serviceCredentials
-	 *            Service credentials
-	 * @param file
-	 *            File
-	 * @param code
-	 *            Code
-	 * @param project
-	 *            Prject
-	 * @throws StatAlgoImporterServiceException
-	 *             Exception
-	 */
 	public void save(ServiceCredentials serviceCredentials, ItemDescription file, String code)
 			throws StatAlgoImporterServiceException {
 		FilesStorage filesStorage = new FilesStorage();
 		filesStorage.saveStringInItem(serviceCredentials.getUserName(), file.getId(), code);
 	}
 
-	/**
+	
-	 * 
-	 * @param serviceCredentials
-	 *            Service credentials
-	 * @param file
-	 *            Description of destination file
-	 * @param code
-	 *            Code to insert in the file
-	 * @param project
-	 *            Project
-	 * @return ItemDescription Item description
-	 * @throws StatAlgoImporterServiceException
-	 *             exception
-	 */
 	public ItemDescription saveNew(ServiceCredentials serviceCredentials, ItemDescription file, String code, String folderId) throws StatAlgoImporterServiceException {
 		Path tempFile = createTempFile(file, code);
-		ItemDescription mainCode = saveInWorkspace(tempFile, serviceCredentials, file, folderId);
+		ItemDescription codeItem = saveInWorkspace(tempFile, serviceCredentials, file, folderId);
-		return mainCode;
+		return codeItem;
 	}
 
 	private Path createTempFile(ItemDescription file, String code) throws StatAlgoImporterServiceException {