From 9ff65e115820bd6f2c572bf7a46408a64b9ca3ad Mon Sep 17 00:00:00 2001
From: Lucio Lelii <lucio.lelii@isti.cnr.it>
Date: Mon, 17 Jul 2017 08:51:24 +0000
Subject: [PATCH] git-svn-id:
 https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineSmartExecutor@151102
 82a268e6-3cf1-43bd-a215-b396298e98cf

---
 .../dataanalysis/executor/rscripts/generic/GenericRScript.java  | 2 +-
 .../gcube/dataanalysis/executor/util/LocalRScriptsManager.java  | 2 +-
 .../org/gcube/dataanalysis/executor/util/RScriptsManager.java   | 2 ++
 3 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/gcube/dataanalysis/executor/rscripts/generic/GenericRScript.java b/src/main/java/org/gcube/dataanalysis/executor/rscripts/generic/GenericRScript.java
index 1fb1fbf..7450e91 100644
--- a/src/main/java/org/gcube/dataanalysis/executor/rscripts/generic/GenericRScript.java
+++ b/src/main/java/org/gcube/dataanalysis/executor/rscripts/generic/GenericRScript.java
@@ -131,7 +131,7 @@ public abstract class GenericRScript extends StandardLocalInfraAlgorithm {
 			LOGGER.debug("Executing the script...");
 			// execute the script in multi-user mode
 
-			environmentalParameters.put("gcube_token",config.getGcubeToken());
+			environmentalParameters.put("gcube_token","\""+config.getGcubeToken()+"\"");
 			
 			Rlog = scriptmanager.executeRScript(config, scriptName, null, environmentalParameters, outputParameters, null, null, inputParameters, scriptMustReturnAFile, uploadScriptOnTheInfrastructureWorkspace, deletefiles, scriptSubfolder);
 			LOGGER.debug("..execution finished!");
diff --git a/src/main/java/org/gcube/dataanalysis/executor/util/LocalRScriptsManager.java b/src/main/java/org/gcube/dataanalysis/executor/util/LocalRScriptsManager.java
index 3eb3df2..a501c50 100644
--- a/src/main/java/org/gcube/dataanalysis/executor/util/LocalRScriptsManager.java
+++ b/src/main/java/org/gcube/dataanalysis/executor/util/LocalRScriptsManager.java
@@ -216,7 +216,7 @@ public class LocalRScriptsManager {
 			bw.write("setwd(\"" + scriptdir + "\")\n");
 			for (String inputparam : inputParameters.keySet()) {
 				String value = inputParameters.get(inputparam);
-				bw.write(inputparam + "=" + value + "\n");
+				bw.write(inputparam + "<<-" + value + "\n");
 			}
 			bw.write("source('" + scriptPath.replace("\\", "/") + "')\n");
 			// bw.write("source('" + originalScriptPath.replace("\\", "/") + "')\n");
diff --git a/src/main/java/org/gcube/dataanalysis/executor/util/RScriptsManager.java b/src/main/java/org/gcube/dataanalysis/executor/util/RScriptsManager.java
index 3224b81..c299dea 100644
--- a/src/main/java/org/gcube/dataanalysis/executor/util/RScriptsManager.java
+++ b/src/main/java/org/gcube/dataanalysis/executor/util/RScriptsManager.java
@@ -12,10 +12,12 @@ import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.UUID;
+
 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.slf4j.Logger;
 
 public class RScriptsManager {