git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineSmartExecutor@149027 82a268e6-3cf1-43bd-a215-b396298e98cf

.classpath

@@ -17,12 +17,12 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7">
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>

pom.xml

@@ -54,7 +54,7 @@
 		<dependency>
 			<groupId>org.gcube.dataanalysis</groupId>
 			<artifactId>ecological-engine</artifactId>
-			<version>[1.8.0-SNAPSHOT,2.0.0-SNAPSHOT)</version>
+			<version>[1.11.0-SNAPSHOT,2.0.0-SNAPSHOT)</version>
 		</dependency>
 		<dependency>
 			<groupId>org.gcube.contentmanagement</groupId>
@@ -75,19 +75,15 @@
 			<groupId>org.gcube.core</groupId>
 			<artifactId>common-scope</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>4.11</version>
+			<scope>test</scope>
+		</dependency>
 	</dependencies>
 	<build>
 		<plugins>
-
-
-			<plugin>
-				<artifactId>maven-compiler-plugin</artifactId>
-				<version>3.1</version>
-				<configuration>
-					<source>1.7</source>
-					<target>1.7</target>
-				</configuration>
-			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
@@ -97,8 +93,6 @@
 				</configuration>
 			</plugin>
 
-
-
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-assembly-plugin</artifactId>

src/main/java/org/gcube/dataanalysis/executor/job/management/DistributedProcessingAgentWPS.java

@@ -11,7 +11,7 @@ import org.gcube.dataanalysis.ecoengine.configuration.INFRASTRUCTURE;
 import org.gcube.dataanalysis.ecoengine.connectors.livemonitor.ResourceLoad;
 import org.gcube.dataanalysis.ecoengine.connectors.livemonitor.Resources;
 import org.gcube.dataanalysis.ecoengine.utils.Operations;
-import org.slf4j.Logger;
+import org.apache.log4j.Logger;
 
 public class DistributedProcessingAgentWPS {
 

src/main/java/org/gcube/dataanalysis/executor/job/management/GenericWorker.java

@@ -17,7 +17,7 @@ import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
 import org.gcube.contentmanager.storageclient.model.protocol.smp.Handler;
 import org.gcube.dataanalysis.ecoengine.interfaces.ActorNode;
 import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalInfraAlgorithm;
-import org.slf4j.Logger;
+import org.apache.log4j.Logger;
 
 public class GenericWorker extends StandardLocalInfraAlgorithm{
 

src/main/java/org/gcube/dataanalysis/executor/job/management/WPSJobManager.java

@@ -171,7 +171,7 @@ public class WPSJobManager {
 				
 			} catch (Exception e) {
 				e.printStackTrace();
-				AnalysisLogger.getLogger().error("WPSJobManager->Task Number {} - Process exception ", taskNumber,e);
+				AnalysisLogger.getLogger().error("WPSJobManager->Task Number "+taskNumber+" - Process exception ", e);
 				exitstatus = GenericWorker.TASK_FAILURE;
 				
 			}finally{

src/main/java/org/gcube/dataanalysis/executor/nodes/transducers/WebApplicationPublisher.java

@@ -8,7 +8,6 @@ import java.util.UUID;
 
 import org.apache.commons.io.FileUtils;
 import org.gcube.contentmanagement.graphtools.utils.MathFunctions;
-import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
 import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
 import org.gcube.dataanalysis.ecoengine.datatypes.ServiceType;
 import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
@@ -17,6 +16,8 @@ import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalInfraAlgorithm;
 import org.gcube.dataanalysis.ecoengine.utils.ZipTools;
 import org.gcube.dataanalysis.executor.util.DataTransferer;
 import org.gcube.dataanalysis.executor.util.InfraRetrieval;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 
 public class WebApplicationPublisher extends StandardLocalInfraAlgorithm{
@@ -25,6 +26,8 @@ public class WebApplicationPublisher extends StandardLocalInfraAlgorithm{
 	private String transferServiceAddress = "";
 	private int transferServicePort = 0;
 	
+	private Logger LOGGER = LoggerFactory.getLogger(WebApplicationPublisher.class);
+	
 	@Override
 	public String getDescription() {
 		return "This algorithm publishes a zip file containing a Web site, based on html and javascript in the e-Infrastructure. It generates a public URL to the application that can be shared.";
@@ -46,10 +49,10 @@ public class WebApplicationPublisher extends StandardLocalInfraAlgorithm{
 		String fileAbsolutePath = config.getParam(FileParam);
 //		String mainPage = config.getParam(MainPageParam);
 		
-		AnalysisLogger.getLogger().debug("scope: "+scope);
+		LOGGER.debug("scope: {}",scope);
-		AnalysisLogger.getLogger().debug("username: "+username);
+		LOGGER.debug("username: {}",username);
-		AnalysisLogger.getLogger().debug("fileAbsolutePath: "+fileAbsolutePath);
+		LOGGER.debug("fileAbsolutePath: {}",fileAbsolutePath);
-//		AnalysisLogger.getLogger().debug("layerTitle: "+mainPage);
+//		LOGGER.debug("layerTitle: "+mainPage);
 		
 		if (scope==null || username==null)
 			throw new Exception ("Service parameters are not set - please contact the Administrators");
@@ -62,14 +65,14 @@ public class WebApplicationPublisher extends StandardLocalInfraAlgorithm{
 		String fileName = f.getName();
        		
 		//unzip the file
-		AnalysisLogger.getLogger().debug("Package is in file "+fileName);
+		LOGGER.debug("Package is in file "+fileName);
 		
 		boolean mkdir = folder.mkdir();
-		AnalysisLogger.getLogger().debug("Sandbox " + folder.getAbsolutePath() + " generated: " + mkdir);
+		LOGGER.debug("Sandbox {} generated: {} ",folder.getAbsolutePath(), mkdir);
-		AnalysisLogger.getLogger().debug("Unzipping package into " + folder.getAbsolutePath());
+		LOGGER.debug("Unzipping package into {}",folder.getAbsolutePath());
 		ZipTools.unZip(f.getAbsolutePath(), folder.getAbsolutePath());
 //		f.delete();
-		AnalysisLogger.getLogger().debug("Package unzipped and original file deleted");
+		LOGGER.debug("Package unzipped and original file deleted");
 		
 		File[] webappfiles = folder.listFiles();
 		//get all files for the upload
@@ -90,9 +93,9 @@ public class WebApplicationPublisher extends StandardLocalInfraAlgorithm{
 			String subpath = allfiles.get(key);
 			subpath = subpath.substring(0,subpath.lastIndexOf("/"));
 			String remotePath = remoteFolder+subpath+"/";
-			AnalysisLogger.getLogger().debug("Uploading "+key+" -> "+remotePath);
+			LOGGER.debug("Uploading {}  -> {}",key,remotePath);
 			
-			long transferout = DataTransferer.transferFileToService(scope, username, transferServiceAddress, transferServicePort, key, remotePath);
+			long transferout = DataTransferer.transferFileToService(scope, username, transferServiceAddress, transferServicePort, key, remotePath).getTransferedBytes();
 			if (transferout<=0){
 				throw new Exception("Error transferring files to the infrastructure ");
 			}
@@ -102,22 +105,22 @@ public class WebApplicationPublisher extends StandardLocalInfraAlgorithm{
 		if (webappfiles.length==1 && webappfiles[0].isDirectory()){
 			producedPage = producedPage + webappfiles[0].getName()+"/";
 		}
-		AnalysisLogger.getLogger().debug("Entry point of the page "+producedPage);
+		LOGGER.debug("Entry point of the page "+producedPage);
       
       //get URL
 		addOutputString("Generated Website - Main URL", producedPage);
 	}catch(Exception e){
-			AnalysisLogger.getLogger().error("an error occurred!",e);
+			LOGGER.error("an error occurred!",e);
 			throw e;
 		}finally{	
 		       //clean everything
 			if (folder.exists()){
-				AnalysisLogger.getLogger().debug("Cleaning folder "+folder);
+				LOGGER.debug("Cleaning folder "+folder);
 				FileUtils.cleanDirectory(folder);
 				FileUtils.deleteDirectory(folder);
 			}
 	}
-		AnalysisLogger.getLogger().debug("Process finished");
+		LOGGER.debug("Process finished");
 		status = 100;
 	}
 
@@ -143,7 +146,7 @@ public class WebApplicationPublisher extends StandardLocalInfraAlgorithm{
 
 	@Override
 	public void shutdown() {
-		AnalysisLogger.getLogger().debug("WebApplicationPublisher - shutdown");
+		LOGGER.debug("WebApplicationPublisher - shutdown");
 	}	
 
 	
@@ -157,23 +160,24 @@ public class WebApplicationPublisher extends StandardLocalInfraAlgorithm{
 		String apacheServiceAddress = apacheAddress.get(0);
 		apacheServiceAddress = apacheServiceAddress.substring(apacheServiceAddress.indexOf("http://")+7);
 		
-		AnalysisLogger.getLogger().debug("Found "+apacheAddress.size()+" services");
+		LOGGER.debug("Found {} services",apacheAddress.size());
-		AnalysisLogger.getLogger().debug("Apache address: "+apacheServiceAddress);
+		LOGGER.debug("Apache address: {}",apacheServiceAddress);
+
 		List<String> dataTransferAddress = InfraRetrieval.retrieveService("agent-service", scope);
 		
 		if (dataTransferAddress.size()==0)
 			throw new Exception("Data Transfer services are not available in scope "+scope);
 		
-		AnalysisLogger.getLogger().debug("Found "+dataTransferAddress.size()+" transfer services");
+		LOGGER.debug("Found {} transfer services",dataTransferAddress.size());
 		
 		int apacheDTPort = 9090; 
 		boolean found = false;
 		for (String datatransferservice:dataTransferAddress){
-			AnalysisLogger.getLogger().debug("Transfer service found");
+			LOGGER.debug("Transfer service found");
 			datatransferservice = datatransferservice.substring(datatransferservice.indexOf("http://")+7);
 			String servicehost = datatransferservice.substring(0,datatransferservice.indexOf(":"));
 			String serviceport = datatransferservice.substring(datatransferservice.indexOf(":")+1,datatransferservice.indexOf("/"));
-			AnalysisLogger.getLogger().debug("Transfer service: "+servicehost+":"+serviceport);
+			LOGGER.debug("Transfer service: {} , {}",servicehost,serviceport);
 			if (apacheServiceAddress.equals(servicehost)){
 				apacheDTPort = Integer.parseInt(serviceport);
 				found = true;
@@ -184,7 +188,7 @@ public class WebApplicationPublisher extends StandardLocalInfraAlgorithm{
 		if (!found)
 			throw new Exception("Apache data transfer has not been found in the same scope of the catalog: "+scope);
 		else
-			AnalysisLogger.getLogger().debug("Transfer service found at address "+apacheServiceAddress+":"+apacheDTPort);
+			LOGGER.debug("Transfer service found at address {} : {}",apacheServiceAddress,apacheDTPort);
 		
 		transferServiceAddress = apacheServiceAddress;
 		transferServicePort = apacheDTPort;

src/main/java/org/gcube/dataanalysis/executor/rscripts/generic/GenericRScript.java

@@ -153,7 +153,7 @@ public abstract class GenericRScript extends StandardLocalInfraAlgorithm {
 				}
 
 			} catch (Exception e) {
-				AnalysisLogger.getLogger().warn("Could not delete sandbox folder {} ",folder.getAbsolutePath(),e);
+				AnalysisLogger.getLogger().warn("Could not delete sandbox folder "+folder.getAbsolutePath(),e);
 			}
 			
 			if (Rlog != null) {
@@ -235,7 +235,7 @@ public abstract class GenericRScript extends StandardLocalInfraAlgorithm {
 					org.gcube.dataanalysis.executor.rscripts.generic.FileUtils.moveFileToDirectory(rowFile, new File(config.getConfigPath()), false);
 					files.add(preparedFile);
 					}catch(Exception e){
-						AnalysisLogger.getLogger().error("error in moving file {} to  {}",rowFile.getAbsolutePath(),preparedFile,e);
+						AnalysisLogger.getLogger().error("error in moving file "+rowFile.getAbsolutePath()+" to "+preparedFile,e);
 						throw e;
 					}
 					break;

src/main/java/org/gcube/dataanalysis/executor/util/DataTransferer.java

@@ -1,14 +1,10 @@
 package org.gcube.dataanalysis.executor.util;
 
 import java.io.File;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Map;
 
 import org.gcube.data.transfer.library.DataTransferClient;
 import org.gcube.data.transfer.library.TransferResult;
 import org.gcube.data.transfer.model.Destination;
-import org.gcube.data.transfer.model.PluginInvocation;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -17,8 +13,12 @@ public class DataTransferer {
 
 	private static final Logger logger = LoggerFactory.getLogger(DataTransferer.class); 	
 
+	public static TransferResult transferFileToService(String scope, String username, String host, int port, String fileAbsolutePath, String remoteFolder) throws Exception {
+		return transferFileToService(scope, username, host, port, fileAbsolutePath, remoteFolder, null);
+	}
+	
 	// returns the number of transferred bytes
-	public static long transferFileToService(String scope, String username, String host, int port, String fileAbsolutePath, String remoteFolder) throws Exception {
+	public static TransferResult transferFileToService(String scope, String username, String host, int port, String fileAbsolutePath, String remoteFolder, String destinationId) throws Exception {
 		logger.debug("Transferring file {} to {}:{} " , fileAbsolutePath, host, port );
 
 		DataTransferClient client=DataTransferClient.getInstanceByEndpoint("http://"+host+":"+port);
@@ -29,21 +29,18 @@ public class DataTransferer {
 
 		//String localfolder = localFile.getParent();
 		String file = localFile.getName();
-		
+				 
-		
-		Map<String,String> params=new HashMap<>();
-		params.put("DESTINATION", remoteFolder);
-		params.put("SOURCE_PARAMETER", PluginInvocation.DESTINATION_FILE_PATH);
-		 
 		Destination dest=new Destination(file);
+		dest.setSubFolder(remoteFolder);
 		
-		TransferResult tranferResult = client.localFile(localFile,dest,Collections.singleton(new PluginInvocation("DECOMPRESS",params)));
+		if(destinationId!=null)
+			dest.setPersistenceId(destinationId);
+		
+		TransferResult transferResult = client.localFile(localFile,dest);
 		
 		logger.debug("Transferring...");
-
 		
-
+		return transferResult;
-		return tranferResult.getTransferedBytes();
 	}
 
 }