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@150998 82a268e6-3cf1-43bd-a215-b396298e98cf

pom.xml

@@ -42,11 +42,11 @@
 		<distroDirectory>distro</distroDirectory>
 		<configDirectory>config</configDirectory>
 		<webappDirectory>${project.build.directory}/${project.build.finalName}</webappDirectory>
-		
+
 		<!-- Java -->
 		<maven.compiler.source>1.7</maven.compiler.source>
-		
+
-		
+
 		<!-- GWT configuration -->
 		<gwtVersion>2.6.1</gwtVersion>
 		<gwtLogVersion>3.3.2</gwtLogVersion>
@@ -255,11 +255,8 @@
 
 
 		<!-- Social -->
-		<!-- <dependency>
+		<!-- <dependency> <groupId>org.gcube.portal</groupId> <artifactId>social-networking-library</artifactId> 
-			<groupId>org.gcube.portal</groupId>
+			<scope>provided</scope> </dependency> -->
-			<artifactId>social-networking-library</artifactId>
-			<scope>provided</scope>
-		</dependency> -->
 		<dependency>
 			<groupId>org.gcube.applicationsupportlayer</groupId>
 			<artifactId>aslsocial</artifactId>

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

@@ -15,10 +15,9 @@ import org.gcube.portlets.user.statisticalalgorithmsimporter.server.file.CodeRea
 import org.gcube.portlets.user.statisticalalgorithmsimporter.server.generator.ProjectBuilder;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.server.generator.ProjectDeploy;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.server.is.BuildSAIDescriptor;
-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.CodeSave;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.server.storage.FilesStorage;
 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;

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

@@ -58,8 +58,7 @@ public class AlgorithmGenerator {
 			return tempFile;
 
 		} catch (IOException e) {
-			logger.error(e.getLocalizedMessage());
+			logger.error(e.getLocalizedMessage(),e);
-			e.printStackTrace();
 			throw new StatAlgoImporterServiceException(e.getLocalizedMessage(),
 					e);
 		}

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

@@ -6,6 +6,7 @@ import javax.servlet.http.HttpServletRequest;
 
 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.DeploySave;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.server.util.ServiceCredentials;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.exception.StatAlgoImporterServiceException;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.info.InfoData;
@@ -41,13 +42,19 @@ public class ProjectDeploy {
 	public void deploy() throws StatAlgoImporterServiceException{
 		InfoGenerator infoGenerator=new InfoGenerator(project, serviceCredentials);
 		InfoData infoData=infoGenerator.readInfo();
+		logger.debug("Deploy Save");
+		DeploySave deploySave=new DeploySave(serviceCredentials, project, infoData);
+		deploySave.save();
 		logger.debug("Send notify");
-		sendNotify(infoData);
+		sendNotify(deploySave.getInfoText());
 	}
 	
-	private void sendNotify(InfoData infoData){
+	private void sendNotify(String body){
 		AlgorithmNotification notify = new AlgorithmNotification(httpServletRequest,
-				serviceCredentials, project, recipients, infoData);
+				serviceCredentials, recipients, body);
 		notify.run();
 	}
+	
+
+	
 }

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/server/social/AlgorithmNotification.java

@@ -17,8 +17,6 @@ import org.gcube.common.homelibrary.home.workspace.exceptions.WorkspaceFolderNot
 import org.gcube.portal.notifications.bean.GenericItemBean;
 import org.gcube.portal.notifications.thread.MessageNotificationsThread;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.server.util.ServiceCredentials;
-import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.info.InfoData;
-import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.project.Project;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -33,17 +31,15 @@ public class AlgorithmNotification extends Thread {
 	private static Logger logger = LoggerFactory.getLogger(AlgorithmNotification.class);
 	private HttpServletRequest httpServletRequest;
 	private ServiceCredentials serviceCredentials;
-	private Project project;
 	private ArrayList<Recipient> recipients;
-	private InfoData infoData;
+	private String body;
 
 	public AlgorithmNotification(HttpServletRequest httpServletRequest, ServiceCredentials serviceCredentials,
-			Project project, ArrayList<Recipient> recipients, InfoData infoData) {
+			ArrayList<Recipient> recipients, String body) {
 		this.serviceCredentials = serviceCredentials;
-		this.project = project;
 		this.recipients = recipients;
 		this.httpServletRequest = httpServletRequest;
-		this.infoData = infoData;
+		this.body=body;
 
 	}
 
@@ -60,19 +56,6 @@ public class AlgorithmNotification extends Thread {
 			List<GenericItemBean> recipients = retrieveRecipients();
 
 			String subject = "[SAI] New software publication requested";
-			String body = "Username: " + serviceCredentials.getUserName() + "\nFull Name: "
-					+ serviceCredentials.getFullName() + "\nEmail: " + serviceCredentials.getEmail() + "\n\nin VRE: "
-					+ serviceCredentials.getScope() + "\n\nhas requested to publish the algorithm: " + "\nLanguage: "
-					+ infoData.getLanguage() + "\nAlgorithm Name: " + infoData.getAlgorithmName() + "\nClass Name: "
-					+ infoData.getClassName() + "\nAlgorithm Description: " + infoData.getAlgorithmDescription()
-					+ "\nAlgorithm Category: " + infoData.getAlgorithmCategory() + "\n\nInterpreter Version: "
-					+ infoData.getInterpreterVersion() + "\n\nwith the following jar: "
-					+ project.getProjectTarget().getProjectDeploy().getCodeJar().getPublicLink() + "\n\nInstaller: "
-					+ "\n./addAlgorithm.sh " + infoData.getAlgorithmName() + " " + infoData.getAlgorithmCategory() + " "
-					+ infoData.getClassName() + " " + serviceCredentials.getScope() + " transducerers N "
-					+ project.getProjectTarget().getProjectDeploy().getCodeJar().getPublicLink() + " \""
-					+ infoData.getAlgorithmDescription() + "\"";
-			
 
 			String messageId;
 

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

@@ -52,8 +52,7 @@ public class CodeSave {
 			return tempFile;
 
 		} catch (IOException e) {
-			logger.error(e.getLocalizedMessage());
+			logger.error(e.getLocalizedMessage(),e);
-			e.printStackTrace();
 			throw new StatAlgoImporterServiceException(e.getLocalizedMessage(), e);
 		}
 	}
@@ -68,8 +67,7 @@ public class CodeSave {
 					Files.newInputStream(tempFile, StandardOpenOption.READ), file.getName(), ALGORITHM_DESCRIPTION,
 					ALGORITHM_MIMETYPE, folderId);
 		} catch (IOException e) {
-			logger.error(e.getLocalizedMessage());
+			logger.error(e.getLocalizedMessage(),e);
-			e.printStackTrace();
 			throw new StatAlgoImporterServiceException(e.getLocalizedMessage(), e);
 		}
 
@@ -78,8 +76,7 @@ public class CodeSave {
 			mainCode = new ItemDescription(mainCodeItem.getId(), mainCodeItem.getName(),
 					mainCodeItem.getOwner().getPortalLogin(), mainCodeItem.getPath(), mainCodeItem.getType().name());
 		} catch (InternalErrorException e) {
-			logger.error(e.getLocalizedMessage());
+			logger.error(e.getLocalizedMessage(),e);
-			e.printStackTrace();
 			throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
 
 		}

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

@@ -0,0 +1,120 @@
+package org.gcube.portlets.user.statisticalalgorithmsimporter.server.storage;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.charset.Charset;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.StandardOpenOption;
+import java.util.Arrays;
+import java.util.List;
+
+import org.gcube.common.homelibrary.home.workspace.WorkspaceItem;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.server.util.ServiceCredentials;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.exception.StatAlgoImporterServiceException;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.info.InfoData;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.project.Project;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.workspace.ItemDescription;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * 
+ * @author Giancarlo Panichi
+ *
+ *
+ */
+public class DeploySave {
+	private static final String ADMIN_USER = "statistical.manager";
+	private static final String CODE_JAR_MIMETYPE = "application/java-archive";
+	private static final String CODE_JAR_DESCRIPTION = "Statistical Algorithm Jar";
+	private static final String DESTINATION_FOLDER = "DataMinerAlgorithms";
+	private static final String TXT_MIMETYPE = "text/plain";
+	private static final String EXTENTION_TXT = ".txt";
+
+	public static final Logger logger = LoggerFactory.getLogger(DeploySave.class);
+	private FilesStorage filesStorage;
+
+	private ServiceCredentials serviceCredentials;
+	private Project project;
+	private InfoData infoData;
+	private String infoText;
+
+	public DeploySave(ServiceCredentials serviceCredentials, Project project, InfoData infoData) {
+		this.serviceCredentials = serviceCredentials;
+		this.project = project;
+		this.infoData = infoData;
+		this.infoText = null;
+		filesStorage = new FilesStorage();
+
+	}
+
+	public void save() throws StatAlgoImporterServiceException {
+		ItemDescription codeJar = project.getProjectTarget().getProjectDeploy().getCodeJar();
+
+		InputStream codeJarInputStream = filesStorage.retrieveItemOnWorkspace(serviceCredentials.getUserName(),
+				codeJar.getId());
+
+		WorkspaceItem codeJarItem = filesStorage.createItemOnWorkspaceHowAdmin(ADMIN_USER, codeJarInputStream,
+				codeJar.getName(), CODE_JAR_DESCRIPTION, CODE_JAR_MIMETYPE, DESTINATION_FOLDER);
+
+		ItemDescription codeJarAdminCopy;
+		try {
+			codeJarAdminCopy = new ItemDescription(codeJarItem.getId(), codeJarItem.getName(),
+					codeJarItem.getOwner().getPortalLogin(), codeJarItem.getPath(), codeJarItem.getType().name());
+			codeJarAdminCopy.setPublicLink(codeJarItem.getPublicLink(false));
+		} catch (Throwable e) {
+			logger.error(e.getLocalizedMessage(), e);
+			throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
+
+		}
+		
+		createInfoText(codeJarAdminCopy);
+		
+		
+		try {
+			int codeJarNamelenght = codeJar.getName().length();
+			String codeJarName;
+			if (codeJarNamelenght > 4) {
+				codeJarName = codeJar.getName().substring(0, codeJarNamelenght - 4);
+			} else {
+				throw new StatAlgoImporterServiceException("Error in code jar name: " + codeJar.getName());
+			}
+
+			Path reportInstallTempFile = Files.createTempFile(codeJarName + "_install", EXTENTION_TXT);
+
+			List<String> lines = Arrays.asList(infoText.split("\\n"));
+			Files.write(reportInstallTempFile, lines, Charset.defaultCharset(), StandardOpenOption.WRITE);
+			logger.debug(reportInstallTempFile.toString());
+			InputStream reportInstallInputStream = Files.newInputStream(reportInstallTempFile);
+			
+		    filesStorage.createItemOnWorkspaceHowAdmin(ADMIN_USER, reportInstallInputStream,
+					codeJarName + "_install.txt", codeJarName + "_install.txt", TXT_MIMETYPE, DESTINATION_FOLDER);
+
+		} catch (IOException e) {
+			logger.error("Error writing report install information: " + e.getLocalizedMessage(), e);
+			throw new StatAlgoImporterServiceException(e.getLocalizedMessage(), e);
+		}
+
+	}
+
+	private void createInfoText(ItemDescription codeJarAdminCopy) {
+		infoText = "Username: " + serviceCredentials.getUserName() + "\nFull Name: " + serviceCredentials.getFullName()
+				+ "\nEmail: " + serviceCredentials.getEmail() + "\n\nin VRE: " + serviceCredentials.getScope()
+				+ "\n\nhas requested to publish the algorithm: " + "\nLanguage: " + infoData.getLanguage()
+				+ "\nAlgorithm Name: " + infoData.getAlgorithmName() + "\nClass Name: " + infoData.getClassName()
+				+ "\nAlgorithm Description: " + infoData.getAlgorithmDescription() + "\nAlgorithm Category: "
+				+ infoData.getAlgorithmCategory() + "\n\nInterpreter Version: " + infoData.getInterpreterVersion()
+				+ "\n\nwith the following original jar: "
+				+ project.getProjectTarget().getProjectDeploy().getCodeJar().getPublicLink() + "\nadmin copy jar: "
+				+ codeJarAdminCopy.getPublicLink() + "\n\nInstaller: " + "\n./addAlgorithm.sh "
+				+ infoData.getAlgorithmName() + " " + infoData.getAlgorithmCategory() + " " + infoData.getClassName()
+				+ " " + serviceCredentials.getScope() + " transducerers N " + codeJarAdminCopy.getPublicLink() + " \""
+				+ infoData.getAlgorithmDescription() + "\"";
+	}
+
+	public String getInfoText() {
+		return infoText;
+	}
+
+}

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

@@ -281,6 +281,41 @@ public class FilesStorage {
 
 	}
 
+	/**
+	 * 
+	 * @param user
+	 *            User
+	 * @param parentName
+	 *            Parent name
+	 * @param name
+	 *            Name
+	 * @return WorkspaceItem
+	 * @throws StatAlgoImporterServiceException
+	 *             Exception
+	 */
+	public WorkspaceItem findInParentName(String user, String parentName, String name)
+			throws StatAlgoImporterServiceException {
+		Workspace ws;
+		try {
+			logger.info("Find by parent name: [user=" + user + ", parentName=" + parentName + ", name=" + name + "]");
+
+			ws = HomeLibrary.getUserWorkspace(user);
+
+			WorkspaceItem parentItem = ws.getItem(parentName);
+			if (!parentItem.isFolder()) {
+				throw new StatAlgoImporterServiceException("No valid folder: " + parentName + "!");
+			}
+
+			return ws.find(name, parentItem.getId());
+
+		} catch (Throwable e) {
+			logger.error("Find by parent name: " + e.getLocalizedMessage(), e);
+			throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
+
+		}
+
+	}
+
 	/**
 	 * 
 	 * @param user
@@ -398,6 +433,7 @@ public class FilesStorage {
 			ws = HomeLibrary.getUserWorkspace(user);
 
 			WorkspaceItem workSpaceItem = ws.getItem(folderId);
+
 			if (!workSpaceItem.isFolder()) {
 				throw new StatAlgoImporterServiceException("Destination is not a folder!");
 			}
@@ -412,6 +448,55 @@ public class FilesStorage {
 		}
 	}
 
+	/**
+	 * 
+	 * @param user
+	 *            User
+	 * @param inputStream
+	 *            InputStream
+	 * @param name
+	 *            Name
+	 * @param description
+	 *            Description
+	 * @param mimeType
+	 *            MimeType
+	 * @param folderName
+	 *            Folder Path
+	 * @return WorkspaceItem
+	 * @throws StatAlgoImporterServiceException
+	 *             Exception
+	 */
+	public WorkspaceItem createItemOnWorkspaceHowAdmin(String user, InputStream inputStream, String name,
+			String description, String mimeType, String folderName) throws StatAlgoImporterServiceException {
+		Workspace ws;
+		try {
+			logger.info("Create item on workspace how admin: [user=" + user + ", name=" + name + ", description="
+					+ description + ", mimeType=" + mimeType + ", folderName=" + folderName + "]");
+
+			ws = HomeLibrary.getUserWorkspace(user);
+			WorkspaceItem root = ws.getRoot();
+			WorkspaceItem folderItem=ws.find(folderName, root.getId());
+
+			if (folderItem==null||!folderItem.isFolder()) {
+				throw new StatAlgoImporterServiceException("Destination "+folderName+" is not a valid folder!");
+			}
+
+			WorkspaceItem codeJar = ws.find(name, folderItem.getId());
+
+			if (codeJar == null) {
+				return ws.createExternalFile(name, description, mimeType, inputStream, folderItem.getId());
+			} else {
+				ws.updateItem(codeJar.getId(), inputStream);
+				return codeJar;
+			}
+
+		} catch (Throwable e) {
+			logger.error("Create item on workspace how admin: " + e.getLocalizedMessage(), e);
+			throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
+
+		}
+	}
+
 	/**
 	 * 
 	 * @param user