git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineSmartExecutor@122705 82a268e6-3cf1-43bd-a215-b396298e98cf
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@ -17,6 +17,7 @@ import org.gcube.common.scope.api.ScopeProvider;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.executor.scripts.OSCommand;
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import org.junit.runner.notification.RunListener;
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public class LocalRScriptsManager {
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@ -50,16 +51,27 @@ public class LocalRScriptsManager {
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this.status = status;
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}
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public static void substituteStringInFile(String file, String newFile, String s, String sub) throws Exception {
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public static void substituteStringInFile(String file, String newFile, String s, String sub, boolean regex) throws Exception {
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BufferedReader br = new BufferedReader(new FileReader(new File(file)));
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BufferedWriter bw = new BufferedWriter(new FileWriter(new File(newFile)));
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String line = br.readLine();
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while (line != null) {
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int idx = line.indexOf(s);
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if (idx >= 0) {
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line = line.replace(s, sub);
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if (!regex) {
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int idx = line.indexOf(s);
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if (idx >= 0) {
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line = line.replace(s, sub);
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}
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}else{
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// AnalysisLogger.getLogger().debug("Matching "+line+" vs "+s);
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if (line.matches(s)){
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AnalysisLogger.getLogger().debug("Matched Input "+s+" line becomes "+sub);
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line = sub;
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}
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}
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bw.write(line + "\n");
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line = br.readLine();
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}
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@ -68,7 +80,8 @@ public class LocalRScriptsManager {
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bw.close();
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}
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public static void printRConsole(Process process) {
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public String printRConsole(Process process) {
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StringBuffer uberbuffer = new StringBuffer();
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try {
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BufferedReader br = new BufferedReader(new InputStreamReader(process.getInputStream()));
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String line = br.readLine();
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@ -78,7 +91,7 @@ public class LocalRScriptsManager {
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sb.append(line + "\n");
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}
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AnalysisLogger.getLogger().debug(sb);
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uberbuffer.append(sb.toString());
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AnalysisLogger.getLogger().debug("---ERRORS---");
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br = new BufferedReader(new InputStreamReader(process.getErrorStream()));
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line = br.readLine();
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@ -89,27 +102,30 @@ public class LocalRScriptsManager {
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sb.append(line + "\n");
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}
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AnalysisLogger.getLogger().debug(sb);
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uberbuffer.append(sb.toString());
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AnalysisLogger.getLogger().debug("---END OF ERRORS---");
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} catch (Exception e) {
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AnalysisLogger.getLogger().debug("---END BY PROCESS INTERRUPTION---");
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}
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return uberbuffer.toString();
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}
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public void executeRScript(AlgorithmConfiguration config, String scriptName, String inputFileURL, HashMap<String, String> inputParameters, String defaultInputFile, String defaultOutputFile, HashMap<String, String> codeInjections, boolean mustReturnAFile, boolean uploadOutputOnStorage, String sandboxFolder) throws Exception {
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executeRScript(config, scriptName, inputFileURL, inputParameters, null, defaultInputFile, defaultOutputFile, codeInjections, mustReturnAFile, uploadOutputOnStorage, true, sandboxFolder);
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executeRScript(config, scriptName, inputFileURL, inputParameters, null, defaultInputFile, defaultOutputFile, codeInjections, mustReturnAFile, uploadOutputOnStorage, true, sandboxFolder);
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}
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public void executeRScript(AlgorithmConfiguration config, String scriptName, String inputFileURL, HashMap<String, String> inputParameters, HashMap<String, String> outputParameters, String defaultInputFile, String defaultOutputFile, HashMap<String, String> codeInjections, boolean mustReturnAFile, boolean uploadOutputOnStorage, String sandboxFolder) throws Exception {
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executeRScript(config, scriptName, inputFileURL, inputParameters, outputParameters, defaultInputFile, defaultOutputFile, codeInjections, mustReturnAFile, uploadOutputOnStorage, true, sandboxFolder);
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executeRScript(config, scriptName, inputFileURL, inputParameters, outputParameters, defaultInputFile, defaultOutputFile, codeInjections, mustReturnAFile, uploadOutputOnStorage, true, sandboxFolder);
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}
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public void executeRScript(AlgorithmConfiguration config, String scriptName, String inputFileURL, HashMap<String, String> inputParameters, String defaultInputFile, String defaultOutputFile, HashMap<String, String> codeInjections, boolean mustReturnAFile, boolean uploadOutputOnStorage, boolean deletefiles, String sandboxFolder) throws Exception {
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executeRScript(config, scriptName, inputFileURL, inputParameters, null, defaultInputFile, defaultOutputFile, codeInjections, mustReturnAFile, uploadOutputOnStorage, deletefiles, sandboxFolder);
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}
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public void executeRScript(AlgorithmConfiguration config, String scriptName, String inputFileURL, HashMap<String, String> inputParameters, HashMap<String, String> outputParameters, String defaultInputFile, String defaultOutputFile, HashMap<String, String> codeInjections, boolean mustReturnAFile, boolean uploadOutputOnStorage, boolean deletefiles, String sandboxFolder) throws Exception {
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public String executeRScript(AlgorithmConfiguration config, String scriptName, String inputFileURL, HashMap<String, String> inputParameters, HashMap<String, String> outputParameters, String defaultInputFile, String defaultOutputFile, HashMap<String, String> codeInjections, boolean mustReturnAFile, boolean uploadOutputOnStorage, boolean deletefiles, String sandboxFolder) throws Exception {
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List<String> tempfiles = new ArrayList<String>();
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String RLog = "";
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try {
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status = 0;
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String scriptPath = new File(sandboxFolder, scriptName).getAbsolutePath();
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@ -143,23 +159,23 @@ public class LocalRScriptsManager {
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String substitution = codeInjections.get(toSubstitute);
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AnalysisLogger.getLogger().debug("Substituting : " + toSubstitute + " with " + substitution);
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preparedScriptPath = new File(sandboxFolder, UUID.randomUUID() + scriptName).getAbsolutePath();
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substituteStringInFile(scriptPath, preparedScriptPath, toSubstitute, substitution);
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AnalysisLogger.getLogger().debug("New Script name: " + preparedScriptPath+" exists: "+new File(preparedScriptPath).exists());
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substituteStringInFile(scriptPath, preparedScriptPath, toSubstitute, substitution,true);
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AnalysisLogger.getLogger().debug("New Script name: " + preparedScriptPath + " exists: " + new File(preparedScriptPath).exists());
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tempfiles.add(preparedScriptPath);
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scriptPath = preparedScriptPath;
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}
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}
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if (defaultInputFile!=null){
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if (defaultInputFile != null) {
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String newInputFile = new File(sandboxFolder, UUID.randomUUID() + defaultInputFile).getAbsolutePath().replace("\\", "/");
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tempfiles.add(newInputFile);
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AnalysisLogger.getLogger().debug("New Input File is " + newInputFile);
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if (inputFileURL.trim().length() > 0) {
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AnalysisLogger.getLogger().debug("Substituting standard Input");
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preparedScriptPath = new File(sandboxFolder, UUID.randomUUID() + scriptName).getAbsolutePath();
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substituteStringInFile(scriptPath, preparedScriptPath, defaultInputFile, newInputFile);
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substituteStringInFile(scriptPath, preparedScriptPath, defaultInputFile, newInputFile,false);
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} else {
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if ((preparedScriptPath==null) || (preparedScriptPath.trim().length()==0))
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if ((preparedScriptPath == null) || (preparedScriptPath.trim().length() == 0))
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preparedScriptPath = new File(sandboxFolder, scriptName).getAbsolutePath();
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}
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@ -176,44 +192,45 @@ public class LocalRScriptsManager {
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String newOutputFile = UUID.randomUUID().toString() + defaultOutputFile;
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String newOutputFilePath = new File(sandboxFolder, newOutputFile).getAbsolutePath().replace("\\", "/");
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if (defaultOutputFile!=null){
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if (defaultOutputFile != null) {
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int extension = defaultOutputFile.lastIndexOf(".");
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if (extension > 0)
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newOutputFile = defaultOutputFile.substring(0, extension) + "_" + UUID.randomUUID().toString() + "." + defaultOutputFile.substring(extension + 1);
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newOutputFilePath = new File(sandboxFolder, newOutputFile).getAbsolutePath().replace("\\", "/");
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AnalysisLogger.getLogger().debug("New Output File is " + newOutputFilePath);
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AnalysisLogger.getLogger().debug("Substituting standard Output");
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preparedScriptPath = new File(sandboxFolder, UUID.randomUUID() + scriptName).getAbsolutePath();
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substituteStringInFile(scriptPath, preparedScriptPath, defaultOutputFile, newOutputFilePath);
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tempfiles.add(preparedScriptPath);
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scriptPath = preparedScriptPath;
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newOutputFilePath = new File(sandboxFolder, newOutputFile).getAbsolutePath().replace("\\", "/");
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AnalysisLogger.getLogger().debug("New Output File is " + newOutputFilePath);
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AnalysisLogger.getLogger().debug("Substituting standard Output");
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preparedScriptPath = new File(sandboxFolder, UUID.randomUUID() + scriptName).getAbsolutePath();
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substituteStringInFile(scriptPath, preparedScriptPath, defaultOutputFile, newOutputFilePath,false);
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tempfiles.add(preparedScriptPath);
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scriptPath = preparedScriptPath;
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}
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AnalysisLogger.getLogger().debug("Executing R script " + scriptPath);
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status = 10;
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// run the R code
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String scriptdir = new File(scriptPath).getParent().replace("\\", "/");
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process = Runtime.getRuntime().exec("R --no-save\n",null,new File(scriptdir));
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process = Runtime.getRuntime().exec("R --no-save\n", null, new File(scriptdir));
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BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(process.getOutputStream()));
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//set the working directory to the one of the script
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bw.write("setwd(\""+scriptdir+"\")\n");
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// set the working directory to the one of the script
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bw.write("setwd(\"" + scriptdir + "\")\n");
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for (String inputparam : inputParameters.keySet()) {
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String value = inputParameters.get(inputparam);
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bw.write(inputparam + "<-" + value + "\n");
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bw.write(inputparam + "=" + value + "\n");
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}
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bw.write("source('" + scriptPath.replace("\\", "/") + "')\n");
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// bw.write("source('" + originalScriptPath.replace("\\", "/") + "')\n");
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if (outputParameters!=null){
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if (outputParameters != null) {
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for (String outputparam : outputParameters.keySet()) {
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bw.write("paste(\"out->\","+outputparam+")"+ "\n");
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bw.write("write.csv("+outputparam+",file=\""+new File(sandboxFolder,outputparam).getAbsolutePath().replace("\\", "/")+"\",row.names=FALSE,append=F,fileEncoding=\"UTF-8\",eol = \"\\n\")"+ "\n");
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bw.write("paste(\"out->\"," + outputparam + ")" + "\n");
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bw.write("write.csv(" + outputparam + ",file=\"" + new File(sandboxFolder, outputparam).getAbsolutePath().replace("\\", "/") + "\",row.names=FALSE,append=F,fileEncoding=\"UTF-8\",eol = \"\\n\")" + "\n");
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}
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}
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bw.write("q()\n");
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bw.close();
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printRConsole(process);
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RLog = printRConsole(process);
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process.destroy();
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if ((new File(newOutputFilePath)).exists()) {
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@ -253,6 +270,8 @@ public class LocalRScriptsManager {
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AnalysisLogger.getLogger().debug("Done: Deleted temp files");
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}
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}
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return RLog;
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}
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public void stop() {
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@ -299,7 +318,7 @@ public class LocalRScriptsManager {
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inputParameters.put("npoints", "10");
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inputParameters.put("equalDist", "TRUE");
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scriptmanager.executeRScript(config, scriptName, inputFileURL, inputParameters, defaultInputFile, defaultOutputFile, null, true, true,"./");
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scriptmanager.executeRScript(config, scriptName, inputFileURL, inputParameters, defaultInputFile, defaultOutputFile, null, true, true, "./");
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}
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}
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