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ecological-engine-smart-executor
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git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineSmartExecutor@151102 82a268e6-3cf1-43bd-a215-b396298e98cf

This commit is contained in:
Lucio Lelii 2017-07-17 08:51:24 +00:00
parent 682364d58b
commit 9ff65e1158
3 changed files with 4 additions and 2 deletions
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2
src/main/java/org/gcube/dataanalysis/executor/rscripts/generic/GenericRScript.java
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@ -131,7 +131,7 @@ public abstract class GenericRScript extends StandardLocalInfraAlgorithm {
LOGGER.debug("Executing the script..."); LOGGER.debug("Executing the script...");
// execute the script in multi-user mode // 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); Rlog = scriptmanager.executeRScript(config, scriptName, null, environmentalParameters, outputParameters, null, null, inputParameters, scriptMustReturnAFile, uploadScriptOnTheInfrastructureWorkspace, deletefiles, scriptSubfolder);
LOGGER.debug("..execution finished!"); LOGGER.debug("..execution finished!");

2
src/main/java/org/gcube/dataanalysis/executor/util/LocalRScriptsManager.java
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@ -216,7 +216,7 @@ public class LocalRScriptsManager {
bw.write("setwd(\"" + scriptdir + "\")\n"); bw.write("setwd(\"" + scriptdir + "\")\n");
for (String inputparam : inputParameters.keySet()) { for (String inputparam : inputParameters.keySet()) {
String value = inputParameters.get(inputparam); String value = inputParameters.get(inputparam);
bw.write(inputparam + "=" + value + "\n"); bw.write(inputparam + "<<-" + value + "\n");
} }
bw.write("source('" + scriptPath.replace("\\", "/") + "')\n"); bw.write("source('" + scriptPath.replace("\\", "/") + "')\n");
// bw.write("source('" + originalScriptPath.replace("\\", "/") + "')\n"); // bw.write("source('" + originalScriptPath.replace("\\", "/") + "')\n");

2
src/main/java/org/gcube/dataanalysis/executor/util/RScriptsManager.java
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@ -12,10 +12,12 @@ import java.util.HashMap;
import java.util.LinkedHashMap; import java.util.LinkedHashMap;
import java.util.List; import java.util.List;
import java.util.UUID; import java.util.UUID;
import org.gcube.common.scope.api.ScopeProvider; import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.executor.scripts.OSCommand; import org.gcube.dataanalysis.executor.scripts.OSCommand;
import org.slf4j.Logger;
public class RScriptsManager { public class RScriptsManager {