git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineSmartExecutor@148375 82a268e6-3cf1-43bd-a215-b396298e98cf

.classpath

@@ -1,9 +1,31 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
+<classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java"/>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
-	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources"/>
+		<attributes>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java"/>
+			<attribute name="optional" value="true"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+			<attribute name="maven.pomderived" value="true"/>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
+		</attributes>
-	<classpathentry kind="output" path="target/classes"/>
+	</classpathentry>
-</classpath>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<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">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

.settings/org.eclipse.jdt.core.prefs

@@ -1,13 +1,12 @@
-#Fri Jun 22 18:05:41 CEST 2012
 eclipse.preferences.version=1
 org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
 org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
-org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.compliance=1.7
 org.eclipse.jdt.core.compiler.debug.lineNumber=generate
 org.eclipse.jdt.core.compiler.debug.localVariable=generate
 org.eclipse.jdt.core.compiler.debug.sourceFile=generate
 org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
 org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
 org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
-org.eclipse.jdt.core.compiler.source=1.6
+org.eclipse.jdt.core.compiler.source=1.7

pom.xml

@@ -9,12 +9,25 @@
 	</parent>
 	<groupId>org.gcube.dataanalysis</groupId>
 	<artifactId>ecological-engine-smart-executor</artifactId>
-	<version>1.4.0-SNAPSHOT</version>
+	<version>1.5.0-SNAPSHOT</version>
 	<name>Smart Ecological Engine Executor</name>
 	<description>Smart Ecological Engine Executor library</description>
 	<scm>
 		<url>https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineSmartExecutor</url>
 	</scm>
+
+	<dependencyManagement>
+		<dependencies>
+			<dependency>
+				<groupId>org.gcube.distribution</groupId>
+				<artifactId>gcube-bom</artifactId>
+				<version>LATEST</version>
+				<type>pom</type>
+				<scope>import</scope>
+			</dependency>
+		</dependencies>
+	</dependencyManagement>
+
 	<developers>
 		<developer>
 			<name>Gianpaolo Coro</name>
@@ -33,16 +46,16 @@
 		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
 	</properties>
 	<dependencies>
+		<dependency>
+			<groupId>org.gcube.data.transfer</groupId>
+			<artifactId>data-transfer-library</artifactId>
+			<version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version>
+		</dependency>
 		<dependency>
 			<groupId>org.gcube.dataanalysis</groupId>
 			<artifactId>ecological-engine</artifactId>
 			<version>[1.8.0-SNAPSHOT,2.0.0-SNAPSHOT)</version>
 		</dependency>
-		<dependency>
-			<groupId>org.gcube.data.transfer</groupId>
-			<artifactId>agent-library</artifactId>
-			<version>[2.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version>
-		</dependency>
 		<dependency>
 			<groupId>org.gcube.contentmanagement</groupId>
 			<artifactId>storage-manager-core</artifactId>
@@ -56,49 +69,23 @@
 		<dependency>
 			<groupId>org.apache.activemq</groupId>
 			<artifactId>activemq-core</artifactId>
-			<version>5.6.0</version>
+			<version>5.7.0</version>
-		</dependency>
-		<dependency>
-			<groupId>org.gcube.common</groupId>
-			<artifactId>common-authorization</artifactId>
-			<version>[2.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version>
-			<scope>provided</scope>
-			<exclusions>
-				<exclusion>
-					<artifactId>slf4j-api</artifactId>
-					<groupId>org.slf4j</groupId>
-				</exclusion>
-				<exclusion>
-					<artifactId>common-utils-encryption</artifactId>
-					<groupId>org.gcube.core</groupId>
-				</exclusion>
-			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>org.gcube.core</groupId>
 			<artifactId>common-scope</artifactId>
-			<version>[1.2.0-SNAPSHOT,2.0.0-SNAPSHOT)</version>
-			<scope>provided</scope>
-			<exclusions>
-				<exclusion>
-					<artifactId>slf4j-api</artifactId>
-					<groupId>org.slf4j</groupId>
-				</exclusion>
-				<!--<exclusion> <artifactId>common-scope-maps</artifactId> <groupId>org.gcube.core</groupId> 
-					</exclusion> -->
-			</exclusions>
 		</dependency>
 	</dependencies>
 	<build>
 		<plugins>
-			
+
-	
+
 			<plugin>
 				<artifactId>maven-compiler-plugin</artifactId>
 				<version>3.1</version>
 				<configuration>
-					<source>1.6</source>
+					<source>1.7</source>
-					<target>1.6</target>
+					<target>1.7</target>
 				</configuration>
 			</plugin>
 			<plugin>
@@ -109,13 +96,12 @@
 					<skipTests>true</skipTests>
 				</configuration>
 			</plugin>
-			
+
-			
+
-			
+
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-assembly-plugin</artifactId>
-				<version>2.2</version>
 				<configuration>
 					<descriptors>
 						<descriptor>${distroDirectory}/descriptor.xml</descriptor>

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

@@ -1,22 +1,17 @@
 package org.gcube.dataanalysis.executor.job.management;
 
-import java.io.File;
-import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
-import org.apache.log4j.Logger;
 import org.gcube.contentmanagement.graphtools.utils.HttpRequest;
 import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
-import org.gcube.contentmanagement.lexicalmatcher.utils.FileTools;
 import org.gcube.dataanalysis.ecoengine.configuration.ALG_PROPS;
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
 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 com.thoughtworks.xstream.XStream;
 
 public class DistributedProcessingAgentWPS {
 

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

@@ -13,11 +13,11 @@ import java.net.URLEncoder;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 
-import org.apache.log4j.Logger;
 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;
 
 public class GenericWorker extends StandardLocalInfraAlgorithm{
 

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

@@ -171,8 +171,7 @@ public class WPSJobManager {
 				
 			} catch (Exception e) {
 				e.printStackTrace();
-				AnalysisLogger.getLogger().debug(e);
+				AnalysisLogger.getLogger().error("WPSJobManager->Task Number {} - Process exception ", taskNumber,e);
-				AnalysisLogger.getLogger().debug("WPSJobManager->Task Number "+taskNumber+" - Process exception: " + e.getLocalizedMessage());
 				exitstatus = GenericWorker.TASK_FAILURE;
 				
 			}finally{

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

@@ -92,8 +92,8 @@ public class WebApplicationPublisher extends StandardLocalInfraAlgorithm{
 			String remotePath = remoteFolder+subpath+"/";
 			AnalysisLogger.getLogger().debug("Uploading "+key+" -> "+remotePath);
 			
-			boolean transferout = DataTransferer.transferFileToService(scope, username, transferServiceAddress, transferServicePort, key, remotePath);
+			long transferout = DataTransferer.transferFileToService(scope, username, transferServiceAddress, transferServicePort, key, remotePath);
-			if (!transferout){
+			if (transferout<=0){
 				throw new Exception("Error transferring files to the infrastructure ");
 			}
 			i++;
@@ -107,9 +107,7 @@ public class WebApplicationPublisher extends StandardLocalInfraAlgorithm{
       //get URL
 		addOutputString("Generated Website - Main URL", producedPage);
 	}catch(Exception e){
-			e.printStackTrace();
+			AnalysisLogger.getLogger().error("an error occurred!",e);
-			AnalysisLogger.getLogger().debug(e);
-			AnalysisLogger.getLogger().debug("An error occurred!");
 			throw e;
 		}finally{	
 		       //clean everything

src/main/java/org/gcube/dataanalysis/executor/nodes/transducers/bionym/BionymLocalTransducer.java

@@ -2,6 +2,7 @@ package org.gcube.dataanalysis.executor.nodes.transducers.bionym;
 
 import java.io.File;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
@@ -25,7 +26,6 @@ import org.gcube.dataanalysis.executor.nodes.transducers.bionym.interfaces.Match
 import org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters;
 import org.gcube.dataanalysis.executor.scripts.OSCommand;
 
-import scala.actors.threadpool.Arrays;
 
 public class BionymLocalTransducer implements Transducerer {
 	// BionymFlexibleWorkflowTransducer bionymwf = new BionymFlexibleWorkflowTransducer();

src/main/java/org/gcube/dataanalysis/executor/nodes/transducers/bionym/abstracts/YasmeenMatcher.java

@@ -5,7 +5,6 @@ import java.security.Permission;
 import java.util.HashMap;
 import java.util.UUID;
 
-import org.apache.tools.ant.ExitException;
 import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
 import org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.LevensteinMatcher;
 import org.gcube.dataanalysis.executor.nodes.transducers.bionym.interfaces.Matcher;
@@ -158,7 +157,7 @@ public abstract class YasmeenMatcher implements Matcher {
 		@Override
 		public void checkExit(int status) {
 			super.checkExit(status);
-			throw new ExitException(status);
+			throw new RuntimeException("exit status is "+status);
 		}
 	}
 }

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

@@ -153,8 +153,7 @@ public abstract class GenericRScript extends StandardLocalInfraAlgorithm {
 				}
 
 			} catch (Exception e) {
-				AnalysisLogger.getLogger().debug(e);
+				AnalysisLogger.getLogger().warn("Could not delete sandbox folder {} ",folder.getAbsolutePath(),e);
-				AnalysisLogger.getLogger().debug("Could not delete sandbox folder " + folder.getAbsolutePath());
 			}
 			
 			if (Rlog != null) {
@@ -236,9 +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){
-						e.printStackTrace();
+						AnalysisLogger.getLogger().error("error in moving file {} to  {}",rowFile.getAbsolutePath(),preparedFile,e);
-						AnalysisLogger.getLogger().debug("error in moving file " + rowFile.getAbsolutePath() + " to " + preparedFile);
-						AnalysisLogger.getLogger().debug(e);
 						throw e;
 					}
 					break;

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

@@ -1,155 +1,49 @@
 package org.gcube.dataanalysis.executor.util;
 
-import static org.gcube.datatransfer.agent.library.proxies.Proxies.transferAgent;
-
 import java.io.File;
-import java.net.URI;
+import java.util.Collections;
-import java.net.URL;
+import java.util.HashMap;
-import java.net.URLEncoder;
+import java.util.Map;
-import java.util.ArrayList;
+
-import java.util.concurrent.TimeUnit;
+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;
 
-import org.gcube.common.scope.api.ScopeProvider;
-import org.gcube.contentmanagement.blobstorage.service.IClient;
-import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
-import org.gcube.contentmanager.storageclient.wrapper.AccessType;
-import org.gcube.contentmanager.storageclient.wrapper.MemoryType;
-import org.gcube.contentmanager.storageclient.wrapper.StorageClient;
-import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
-import org.gcube.datatransfer.agent.library.AgentLibrary;
-import org.gcube.datatransfer.agent.library.exceptions.MonitorTransferException;
-import org.gcube.datatransfer.common.agent.Types.storageType;
-import org.gcube.datatransfer.common.options.TransferOptions;
-import org.gcube.datatransfer.common.outcome.FileTransferOutcome;
-import org.gcube.datatransfer.common.outcome.TransferStatus;
 
 public class DataTransferer {
 
-	public static void main(String[] args) throws Exception {
+	private static final Logger logger = LoggerFactory.getLogger(DataTransferer.class); 	
-		//String scope = "/d4science.research-infrastructures.eu/gCubeApps";
-		
-		String scope = "/gcube/devsec/devVRE";
-		//test only ScopeProvider.instance.set(scope);
-		//String transferGHN = "dewn04.madgik.di.uoa.gr";
-		String transferGHN = "access.d4science.org";
-		int transferPort = 8080;
-		AgentLibrary library = transferAgent().at(transferGHN, transferPort).build();
-
-		ArrayList<URI> input = new ArrayList<URI>();
-		/*
-		 * File localfile = new File("C:/Users/coro/Dropbox/Public/wind1.tif"); String file = "wind1.tif"; String localfolder = "C:/Users/coro/Dropbox/Public/"; String storagesmpurl = StorageUtils.uploadFilesOnStorage("/gcube/devsec", "gianpaolo.coro",localfolder,file);
-		 * 
-		 * System.out.println("URI from storage: "+storagesmpurl);
-		 * 
-		 * String urlStorage = "http://dev.d4science.org/uri-resolver/smp?smp-uri="+storagesmpurl+"&fileName="+file;
-		 */
-		// String urlStorage = "http://dev.d4science.org/smp?smp-uri=smp://data.gcube.org/gzAv/RparhTHO4yhbF9ItALcRlSJRIiBGmbP5+HKCzc=&fileName=wind1.tif";
-		//String urlStorage = "http://data.gcube.org/gzAv/RparhTHO4yhbF9ItALcRlSJRIiBGmbP5+HKCzc=";
-		String urlStorage ="http://goo.gl/Vq8QVY";
-
-		System.out.println("URL for storage: " + urlStorage);
-
-		URI uri = new URI("http://dl.dropboxusercontent.com/u/12809149/wind1.tif");
-		// URI uri = new URI(urlStorage);
-
-		// http://dev.d4science.org/uri-resolver/smp?smp-uri=smp://data.gcube.org/gzAv/RparhTHO4yhbF9ItALcRlSJRIiBGmbP5+HKCzc=&fileName=wind1.tif&contentType=tiff
-
-		// URI uri = new URI(storageurl); //localfile.toURI();
-		// URI uri = new URI("file:///C:Users/coro/Dropbox/Public/wind1.tif");
-		input.add(uri);
-
-		//String outPath = "/tmp";
-		String outPath = "/var/www/html/test/";
-		String fileToTransfer = "C:\\Users\\coro\\Dropbox\\Public\\3_Aquamaps.jpg";
-		//fileToTransfer = "C:\\Users\\coro\\Dropbox\\Public\\3_Aquamaps.jpg";
-//		fileToTransfer = "C:/Users/coro/Desktop/DATABASE e NOTE/Experiments/WEB_APP_PUBLISHER/gcube/images/Resource Model.png";
-		transferFileToService(scope, "gianpaolo.coro", transferGHN, transferPort,fileToTransfer , outPath);
-		
-		
-	}
 
 	// returns the number of transferred bytes
-	public static boolean transferFileToService(String scope, String username, String service, int port, String fileAbsolutePath, String remoteFolder) throws Exception {
+	public static long transferFileToService(String scope, String username, String host, int port, String fileAbsolutePath, String remoteFolder) throws Exception {
-		AnalysisLogger.getLogger().debug("Transferring file " + fileAbsolutePath + " to " + service + ":" + port);
+		logger.debug("Transferring file {} to {}:{} " , fileAbsolutePath, host, port );
-//		ScopeProvider.instance.set(scope);
+
+		DataTransferClient client=DataTransferClient.getInstanceByEndpoint("http://"+host+":"+port);
 
-		AgentLibrary library = transferAgent().at(service, port).build();
-		ArrayList<URI> input = new ArrayList<URI>();
 		File localFile = new File(fileAbsolutePath);
 		if (!localFile.exists())
 			throw new Exception("Local file does not exist: " + localFile);
 
-		String localfolder = localFile.getParent();
+		//String localfolder = localFile.getParent();
 		String file = localFile.getName();
-		AnalysisLogger.getLogger().debug("Uploading file " + file + " onto storage");
-//		ScopeProvider.instance.set(scope);
-		AnalysisLogger.getLogger().info("Loading file on scope: " + scope);
-		
-		String storagesmpurl = StorageUtils.uploadFilesOnStorage(scope, username, localfolder, "/",file,true);
-		//urls for testing
-		//storagesmpurl = "http://dev.d4science.org/smp?smp-uri="+storagesmpurl+"&fileName="+file;
-		//	String storagesmpurl = "smp://data.gcube.org/sHtVhK4clGtbcWCliQud+5b4PfGx5BW+GmbP5+HKCzc=";
-		//	String storagesmpurl = "http://goo.gl/r6ggMA";
-		//	String storagesmpurl = "http://dl.dropboxusercontent.com/u/12809149/3_Aquamaps.jpg";
-		
-		AnalysisLogger.getLogger().debug("SMP url generated: " + storagesmpurl);
-		URI uri = new URI(storagesmpurl);
-		input.add(uri);
-
-		TransferOptions options = new TransferOptions();
-
-		options = new TransferOptions();
-		options.setOverwriteFile(false);
-		options.setType(storageType.DataStorage);
-		options.setUnzipFile(false);
-		options.setTransferTimeout(3, TimeUnit.HOURS);
-		AnalysisLogger.getLogger().debug("Transferring...");
-
-		//old code for sync transfer
-//		ArrayList<FileTransferOutcome> outcomes = library.startTransferSync(input, remoteFolder, options);
 		
 		
-		ArrayList<URI> outputURI = new ArrayList<URI>();
+		Map<String,String> params=new HashMap<>();
-//		outputURI.add(new URI("file://"+remoteFolder.replace(" ", "_")+file.replace(" ", "_")));
+		params.put("DESTINATION", remoteFolder);
-		outputURI.add(new URI("file://"+remoteFolder.replace(" ", "%20")+file.replace(" ", "%20")));
+		params.put("SOURCE_PARAMETER", PluginInvocation.DESTINATION_FILE_PATH);
+		 
+		Destination dest=new Destination(file);
 		
-		AnalysisLogger.getLogger().debug("Remote file name will be: " + outputURI.get(0));
+		TransferResult tranferResult = client.localFile(localFile,dest,Collections.singleton(new PluginInvocation("DECOMPRESS",params)));
 		
-		String transferId = library.startTransfer(input, outputURI, options);
+		logger.debug("Transferring...");
 
-		TransferStatus transferStatus = null;
+		
 
-		do {
+		return tranferResult.getTransferedBytes();
-			try {
-
-				Thread.sleep(1000);
-				transferStatus = TransferStatus.valueOf(library.monitorTransfer(transferId));
-
-			} catch (MonitorTransferException e) {
-				e.printStackTrace();
-			}
-
-		} while (!transferStatus.hasCompleted());
-
-		ArrayList<FileTransferOutcome> outcomes = library.getTransferOutcomes(transferId, FileTransferOutcome.class);
-
-		AnalysisLogger.getLogger().debug("Transferring complete");
-		boolean success = false;
-		String outcomeString = "";
-		for (FileTransferOutcome outcome : outcomes) {
-			AnalysisLogger.getLogger().debug("Outcome " + outcome);
-			outcomeString = outcome.toString();
-			AnalysisLogger.getLogger().debug("Transferred file name " + outcome.fileName());
-			AnalysisLogger.getLogger().debug("Transferring success " + outcome.isSuccess());
-			AnalysisLogger.getLogger().debug("Transferred bytes " + outcome.getTotal_size());
-			AnalysisLogger.getLogger().debug("Transfer time " + outcome.getTransferTime());
-			success = outcome.isSuccess();
-		}
-
-		if (!success)
-			throw new Exception("No Bytes were transferred to the Thredds server: "+outcomeString);
-
-		return success;
 	}
 
 }

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

@@ -17,7 +17,6 @@ import org.gcube.common.scope.api.ScopeProvider;
 import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
 import org.gcube.dataanalysis.executor.scripts.OSCommand;
-import org.junit.runner.notification.RunListener;
 
 public class LocalRScriptsManager {
 
@@ -91,7 +90,7 @@ public class LocalRScriptsManager {
 				line = br.readLine();
 				sb.append(line + "\n");
 			}
-			AnalysisLogger.getLogger().debug(sb);
+			AnalysisLogger.getLogger().debug(sb.toString());
 			uberbuffer.append(sb.toString());
 			AnalysisLogger.getLogger().debug("---ERRORS---");
 			br = new BufferedReader(new InputStreamReader(process.getErrorStream()));
@@ -102,7 +101,7 @@ public class LocalRScriptsManager {
 				line = br.readLine();
 				sb.append(line + "\n");
 			}
-			AnalysisLogger.getLogger().debug(sb);
+			AnalysisLogger.getLogger().debug(sb.toString());
 			uberbuffer.append(sb.toString());
 			AnalysisLogger.getLogger().debug("---END OF ERRORS---");
 		} catch (Exception e) {
@@ -284,7 +283,8 @@ public class LocalRScriptsManager {
 			}
 		}
 	}
-
+	
+	/*
 	public static void main1(String[] args) throws Exception {
 		String url = StorageUtils.uploadFilesOnStorage("/gcube/devsec/devVRE", "ecological.engine", "C:\\Users\\coro\\Documents\\", "tacsatmini.csv");
 		System.out.println(url);
@@ -321,5 +321,5 @@ public class LocalRScriptsManager {
 
 		scriptmanager.executeRScript(config, scriptName, inputFileURL, inputParameters, defaultInputFile, defaultOutputFile, null, true, true, "./");
 	}
-
+*/
 }

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

@@ -12,8 +12,6 @@ import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.UUID;
-
-import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
 import org.gcube.common.scope.api.ScopeProvider;
 import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
@@ -78,7 +76,7 @@ public class RScriptsManager {
 				line = br.readLine();
 				sb.append(line + "\n");
 			}
-			AnalysisLogger.getLogger().debug(sb);
+			AnalysisLogger.getLogger().debug(sb.toString());
 
 			AnalysisLogger.getLogger().debug("---ERRORS---");
 			br = new BufferedReader(new InputStreamReader(process.getErrorStream()));
@@ -89,7 +87,7 @@ public class RScriptsManager {
 				line = br.readLine();
 				sb.append(line + "\n");
 			}
-			AnalysisLogger.getLogger().debug(sb);
+			AnalysisLogger.getLogger().debug(sb.toString());
 			AnalysisLogger.getLogger().debug("---END OF ERRORS---");
 		} catch (Exception e) {
 			AnalysisLogger.getLogger().debug("---END BY PROCESS INTERRUPTION---");

src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestBiOnym.java

@@ -1,6 +1,5 @@
 package org.gcube.dataanalysis.executor.tests;
 
-import org.gcube.common.authorization.library.provider.AuthorizationProvider;
 import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
 import org.gcube.common.scope.api.ScopeProvider;
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
@@ -13,7 +12,7 @@ public class RegressionTestBiOnym {
 	public static void executeWF(String[] args) throws Exception {
 		// Generate
 		AlgorithmConfiguration config = new AlgorithmConfiguration();
-		config.setConfigPath("./cfg/");
+		config.setConfigPath("./cfg/");	
 		
 		config.setParam("DatabaseUserName","utente");
 		config.setParam("DatabasePassword","d4science");

src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestCMSY.java

@@ -6,7 +6,6 @@ import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
 import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
 import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory;
-import org.gcube.dataanalysis.ecoengine.test.regression.Regressor;
 
 public class RegressionTestCMSY {
 	/**

src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestFAOMSY.java

@@ -7,7 +7,6 @@ import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
 import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
 import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
 import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory;
-import org.gcube.dataanalysis.ecoengine.test.regression.Regressor;
 import org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing;
 
 public class RegressionTestFAOMSY {

src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestGenerators.java

@@ -4,9 +4,7 @@ import java.util.List;
 
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
 import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
-import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
 import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory;
-import org.gcube.dataanalysis.ecoengine.test.regression.Regressor;
 
 public class RegressionTestGenerators {
 	/**
@@ -20,7 +18,7 @@ public class RegressionTestGenerators {
 
 		List<ComputationalAgent> generators = GeneratorsFactory.getGenerators(testAquamapsSuitable());
 		generators.get(0).init();
-		Regressor.process(generators.get(0));
+		CustomRegressor.process(generators.get(0));
 		generators = null;
 
 	}

src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestICCATVPA.java

@@ -6,8 +6,6 @@ import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
 import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
 import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory;
-import org.gcube.dataanalysis.ecoengine.test.regression.Regressor;
-import org.gcube.dataanalysis.ecoengine.utils.IOHelper;
 
 public class RegressionTestICCATVPA {
 	/**

src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestLWR.java

@@ -6,7 +6,6 @@ import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
 import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
 import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory;
-import org.gcube.dataanalysis.ecoengine.test.regression.Regressor;
 
 public class RegressionTestLWR {
 	/**

src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestTransducers.java

@@ -5,9 +5,7 @@ import java.util.List;
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
 import org.gcube.dataanalysis.ecoengine.evaluation.bioclimate.InterpolateTables.INTERPOLATIONFUNCTIONS;
 import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
-import org.gcube.dataanalysis.ecoengine.interfaces.Transducerer;
 import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory;
-import org.gcube.dataanalysis.ecoengine.test.regression.Regressor;
 
 public class RegressionTestTransducers {
 	
@@ -48,14 +46,14 @@ public static void main(String[] args) throws Exception {
 		*/
 		trans = TransducerersFactory.getTransducerers(testConfigLocal5());
 		trans.get(0).init();
-		Regressor.process(trans.get(0));
+		CustomRegressor.process(trans.get(0));
 		trans = null;
 }
 
 	
 	private static AlgorithmConfiguration testConfigLocal() {
 		
-		AlgorithmConfiguration config = Regressor.getConfig();
+		AlgorithmConfiguration config = CustomRegressor.getConfig();
 		config.setAgent("BIOCLIMATE_HSPEC");
 		config.setParam("HSPEC_TABLE_LIST", "hspec_validation"+AlgorithmConfiguration.getListSeparator()+"hspec_validation2");
 		config.setParam("HSPEC_TABLE_NAMES", "test"+AlgorithmConfiguration.getListSeparator()+"test");
@@ -66,7 +64,7 @@ public static void main(String[] args) throws Exception {
 	
 	private static AlgorithmConfiguration testConfigLocal2() {
 		
-		AlgorithmConfiguration config = Regressor.getConfig();
+		AlgorithmConfiguration config = CustomRegressor.getConfig();
 		config.setAgent("BIOCLIMATE_HCAF");
 		config.setParam("HCAF_TABLE_LIST","hcaf_d"+AlgorithmConfiguration.getListSeparator()+"hcaf_d_2016_linear_01332632269756"+AlgorithmConfiguration.getListSeparator()+"hcaf_d_2016_linear_01336062995861"+AlgorithmConfiguration.getListSeparator()+"hcaf_d_2050");
 		config.setParam("HCAF_TABLE_NAMES", 	"test"+AlgorithmConfiguration.getListSeparator()+"test"+AlgorithmConfiguration.getListSeparator()+"test"+AlgorithmConfiguration.getListSeparator()+"test");
@@ -76,7 +74,7 @@ public static void main(String[] args) throws Exception {
 	
 	private static AlgorithmConfiguration testConfigLocal3() {
 		
-		AlgorithmConfiguration config = Regressor.getConfig();
+		AlgorithmConfiguration config = CustomRegressor.getConfig();
 		config.setAgent("BIOCLIMATE_HSPEN");
 		config.setParam("HSPEN_TABLE_LIST","hspen"+AlgorithmConfiguration.getListSeparator()+"hspen_2016"+AlgorithmConfiguration.getListSeparator()+"hspen_2020"+AlgorithmConfiguration.getListSeparator()+"hspen_2050");
 		config.setParam("HSPEN_TABLE_NAMES", 	"test"+AlgorithmConfiguration.getListSeparator()+"test"+AlgorithmConfiguration.getListSeparator()+"test"+AlgorithmConfiguration.getListSeparator()+"test");
@@ -87,7 +85,7 @@ public static void main(String[] args) throws Exception {
 	
 	private static AlgorithmConfiguration testConfigLocal4() {
 		
-		AlgorithmConfiguration config = Regressor.getConfig();
+		AlgorithmConfiguration config = CustomRegressor.getConfig();
 		config.setAgent("HCAF_INTERPOLATION");
 		
 		config.setParam("FirstHCAF","hcaf_d");
@@ -102,7 +100,7 @@ public static void main(String[] args) throws Exception {
 	
 	private static AlgorithmConfiguration testConfigLocal5() {
 		
-		AlgorithmConfiguration config = Regressor.getConfig();
+		AlgorithmConfiguration config = CustomRegressor.getConfig();
 		config.setAgent("OCCURRENCES_MERGER");
 		
 		config.setParam("longitudeColumn", "decimallongitude");
@@ -125,7 +123,7 @@ public static void main(String[] args) throws Exception {
 	
 	private static AlgorithmConfiguration testConfigLocal6() {
 		
-		AlgorithmConfiguration config = Regressor.getConfig();
+		AlgorithmConfiguration config = CustomRegressor.getConfig();
 		config.setAgent("OCCURRENCES_INSEAS_ONEARTH");
 		
 		config.setParam("longitudeColumn", "decimallongitude");
@@ -140,7 +138,7 @@ public static void main(String[] args) throws Exception {
 
 	private static AlgorithmConfiguration testConfigLocal7() {
 		
-		AlgorithmConfiguration config = Regressor.getConfig();
+		AlgorithmConfiguration config = CustomRegressor.getConfig();
 		config.setAgent("OCCURRENCES_DUPLICATE_DELETER");
 		
 		config.setParam("longitudeColumn", "decimallongitude");

src/test/java/org/gcube/dataanalysis/executor/tests/TestBiOnymLocal.java

@@ -1,15 +1,11 @@
 package org.gcube.dataanalysis.executor.tests;
 
-import java.io.File;
 import java.util.List;
 
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
 import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
 import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
-import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory;
 import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory;
-import org.gcube.dataanalysis.ecoengine.test.regression.Regressor;
-import org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing;
 import org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer;
 import org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymLocalTransducer;
 import org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters;
@@ -67,7 +63,7 @@ public class TestBiOnymLocal {
 		
 		List<StatisticalType> types = transducer.getInputParameters();
 //		System.out.println(types);
-		Regressor.process(transducer);
+		CustomRegressor.process(transducer);
 	}
 	
 }

src/test/java/org/gcube/dataanalysis/executor/tests/TestBiOnymLocalFastVersion.java

@@ -1,15 +1,11 @@
 package org.gcube.dataanalysis.executor.tests;
 
-import java.io.File;
 import java.util.List;
 
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
 import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
 import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
-import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory;
 import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory;
-import org.gcube.dataanalysis.ecoengine.test.regression.Regressor;
-import org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing;
 import org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer;
 import org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymLocalTransducer;
 import org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters;
@@ -48,7 +44,7 @@ public class TestBiOnymLocalFastVersion {
 		
 		List<StatisticalType> types = transducer.getInputParameters();
 
-		Regressor.process(transducer);
+		CustomRegressor.process(transducer);
 	}
 	
 }

src/test/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps2_1.java

@@ -1,19 +1,14 @@
 package org.gcube.dataanalysis.executor.tests;
 
-import java.io.File;
-
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
-import org.gcube.dataanalysis.ecoengine.test.regression.Regressor;
-import org.gcube.dataanalysis.ecoengine.utils.Transformations;
 import org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing;
-import org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode;
 
 public class TestD4ScienceQueueMaps2_1 {
 
 	public static void main(String[] args) throws Exception {
 		String scope = "/gcube";
 		
-		AlgorithmConfiguration config = Regressor.getConfig();
+		AlgorithmConfiguration config = CustomRegressor.getConfig();
 		config.setConfigPath("./cfg/");
 		config.setPersistencePath("./");
 		

src/test/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps2_2.java

@@ -1,18 +1,6 @@
 package org.gcube.dataanalysis.executor.tests;
 
-import java.util.ArrayList;
-import java.util.List;
-
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
-import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
-import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
-import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
-import org.gcube.dataanalysis.ecoengine.datatypes.ServiceType;
-import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
-import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
-import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.ServiceParameters;
-import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
-import org.gcube.dataanalysis.ecoengine.test.regression.Regressor;
 import org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing;
 
 public class TestD4ScienceQueueMaps2_2 {
@@ -30,7 +18,7 @@ public class TestD4ScienceQueueMaps2_2 {
 		String finalDistributionTable = "hspec_suitable_executorsingle_t3";
 
 		// Generate
-		AlgorithmConfiguration config = Regressor.getConfig();
+		AlgorithmConfiguration config = CustomRegressor.getConfig();
 		
 		config.setParam("DatabaseUserName","utente");
 		config.setParam("DatabasePassword","d4science");

src/test/java/org/gcube/dataanalysis/executor/tests/TestKnitrCompiler.java

@@ -8,7 +8,6 @@ import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
 import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
 import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
 import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory;
-import org.gcube.dataanalysis.ecoengine.test.regression.Regressor;
 
 public class TestKnitrCompiler {
 
@@ -35,7 +34,7 @@ public class TestKnitrCompiler {
 		//init the transducerer
 		transducer.init();
 		//start the process
-		Regressor.process(transducer);
+		CustomRegressor.process(transducer);
 		//retrieve the output
 		StatisticalType st = transducer.getOutput();
 		System.out.println("st:"+((PrimitiveType)st).getContent());

src/test/java/org/gcube/dataanalysis/executor/tests/TestSGVMInterpolation.java

@@ -7,7 +7,6 @@ import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
 import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
 import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
 import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory;
-import org.gcube.dataanalysis.ecoengine.test.regression.Regressor;
 
 public class TestSGVMInterpolation {
 
@@ -46,7 +45,7 @@ public class TestSGVMInterpolation {
 		//init the transducerer
 		transducer.init();
 		//start the process
-		Regressor.process(transducer);
+		CustomRegressor.process(transducer);
 		//retrieve the output
 		StatisticalType st = transducer.getOutput();
 		System.out.println("st:"+((PrimitiveType)st).getContent());

src/test/java/org/gcube/dataanalysis/executor/tests/TestWebAppPublisher.java

@@ -7,7 +7,6 @@ import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
 import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
 import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
 import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory;
-import org.gcube.dataanalysis.ecoengine.test.regression.Regressor;
 
 public class TestWebAppPublisher {
 
@@ -35,7 +34,7 @@ public class TestWebAppPublisher {
 		List<ComputationalAgent> trans = null;
 		trans = TransducerersFactory.getTransducerers(config);
 		trans.get(0).init();
-		Regressor.process(trans.get(0));
+		CustomRegressor.process(trans.get(0));
 		StatisticalType st = trans.get(0).getOutput();
 		AnalysisLogger.getLogger().debug("ST:" + st);
 		trans = null;

target/maven-archiver/pom.properties

@@ -1,5 +0,0 @@
-#Generated by Maven
-#Wed Jun 24 16:37:14 CEST 2015
-version=1.1.0-SNAPSHOT
-groupId=org.gcube.dataanalysis
-artifactId=ecological-engine-smart-executor

target/profile.xml

@@ -1,25 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<Resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-	<ID></ID>
-	<Type>Library</Type>
-	<Profile>
-		<Description>Ecological Engine Executor Library</Description>
-		<Class>EcologicalEngineExecutor</Class>
-		<Name>ecological-engine-smart-executor</Name>
-		<Version>1.0.0</Version>
-		<Packages>
-			<Software>
-				<Name>ecological-engine-smart-executor</Name>
-				<Version>1.1.0-SNAPSHOT</Version>
-				<MavenCoordinates>
-					<groupId>org.gcube.dataanalysis</groupId>
-					<artifactId>ecological-engine-smart-executor</artifactId>
-					<version>1.1.0-SNAPSHOT</version>
-				</MavenCoordinates>
-				<Files>
-					<File>ecological-engine-smart-executor-1.1.0-SNAPSHOT.jar</File>
-				</Files>
-			</Software>
-		</Packages>
-	</Profile>
-</Resource>