326 lines
14 KiB
Java
326 lines
14 KiB
Java
package org.gcube.dataanalysis.executor.util;
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import java.io.BufferedReader;
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import java.io.BufferedWriter;
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import java.io.File;
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import java.io.FileReader;
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import java.io.FileWriter;
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import java.io.InputStreamReader;
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import java.io.OutputStreamWriter;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.LinkedHashMap;
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import java.util.List;
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import java.util.UUID;
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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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public class LocalRScriptsManager {
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public float status = 0;
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public String currentOutputURL;
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Process process;
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public String getCurrentOutputURL() {
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return currentOutputURL;
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}
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public void setCurrentOutputURL(String currentOutputURL) {
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this.currentOutputURL = currentOutputURL;
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}
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public String currentOutputFileName;
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public String getCurrentOutputFileName() {
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return currentOutputFileName;
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}
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public void setCurrentOutputFileName(String currentOutputFileName) {
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this.currentOutputFileName = currentOutputFileName;
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}
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public float getStatus() {
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return status;
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}
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public void setStatus(float status) {
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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, 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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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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br.close();
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bw.close();
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}
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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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StringBuffer sb = new StringBuffer();
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while (line != null) {
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line = br.readLine();
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sb.append(line + "\n");
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}
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AnalysisLogger.getLogger().debug(sb.toString());
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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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sb = new StringBuffer();
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while (line != null) {
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line = br.readLine();
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sb.append(line + "\n");
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}
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AnalysisLogger.getLogger().debug(sb.toString());
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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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}
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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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}
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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 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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// String originalScriptPath = scriptPath;
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String preparedScriptPath = null;
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String owner = config.getParam("ServiceUserName");
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if (owner == null)
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owner = "ecological.engine";
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String scope = config.getGcubeScope();
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if (scope == null)
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scope = ScopeProvider.instance.get();
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AnalysisLogger.getLogger().debug("Current User: " + owner);
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AnalysisLogger.getLogger().debug("Current Scope: " + scope);
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AnalysisLogger.getLogger().debug("Sandbox Folder: " + sandboxFolder);
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AnalysisLogger.getLogger().debug("Script : " + scriptPath);
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AnalysisLogger.getLogger().debug("Prepared Script : " + preparedScriptPath);
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try {
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OSCommand.ExecuteGetLine("ls", null);
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OSCommand.ExecuteGetLine("pwd", null);
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OSCommand.ExecuteGetLine("chmod +x * | whoami", null);
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} catch (Throwable e) {
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AnalysisLogger.getLogger().debug("Cannot execute SO commands");
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}
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if (codeInjections != null) {
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for (String toSubstitute : codeInjections.keySet()) {
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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,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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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,false);
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} else {
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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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AnalysisLogger.getLogger().debug("Creating local file from remote file");
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if (inputFileURL.startsWith("http:") || inputFileURL.startsWith("smp:")) {
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StorageUtils.downloadInputFile(inputFileURL, newInputFile);
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} else if (inputFileURL.trim().length() > 0) {
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OSCommand.FileCopy(inputFileURL, newInputFile);
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}
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tempfiles.add(preparedScriptPath);
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scriptPath = preparedScriptPath;
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}
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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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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,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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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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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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}
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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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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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}
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}
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bw.write("q()\n");
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bw.close();
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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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if (uploadOutputOnStorage) {
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AnalysisLogger.getLogger().debug("Found output file ... saving on the workspace");
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String outputURL = StorageUtils.uploadFilesOnStorage(scope, owner, sandboxFolder, newOutputFile);
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currentOutputURL = outputURL;
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AnalysisLogger.getLogger().debug("Output URL is " + outputURL);
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}
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currentOutputFileName = newOutputFilePath;
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AnalysisLogger.getLogger().debug("Output File is " + currentOutputFileName);
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} else if (!mustReturnAFile) {
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AnalysisLogger.getLogger().debug("No file detected as output");
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currentOutputFileName = null;
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currentOutputURL = null;
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} else
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throw new Exception("The script did not return an output - an error occurred");
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AnalysisLogger.getLogger().debug("The procedure was successful");
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status = 100f;
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} catch (Exception e) {
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e.printStackTrace();
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AnalysisLogger.getLogger().debug("The R Script generated an error! " + e.getLocalizedMessage());
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throw e;
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} finally {
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if (deletefiles) {
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AnalysisLogger.getLogger().debug("Deleting temp files");
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for (String file : tempfiles) {
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boolean deleted = new File(file).delete();
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AnalysisLogger.getLogger().debug("Deleting " + file + " " + deleted);
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}
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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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if (process != null) {
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try {
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process.destroy();
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} catch (Exception e) {
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}
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}
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}
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/*
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public static void main1(String[] args) throws Exception {
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String url = StorageUtils.uploadFilesOnStorage("/gcube/devsec/devVRE", "ecological.engine", "C:\\Users\\coro\\Documents\\", "tacsatmini.csv");
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System.out.println(url);
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}
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public static void main(String[] args) throws Exception {
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LocalRScriptsManager scriptmanager = new LocalRScriptsManager();
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AnalysisLogger.setLogger("./cfg/" + AlgorithmConfiguration.defaultLoggerFile);
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AlgorithmConfiguration config = new AlgorithmConfiguration();
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config.setGcubeScope("/gcube/devsec/devVRE");
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config.setPersistencePath("./PARALLEL_PROCESSING");
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String scriptName = "interpolateTacsat.r";
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String inputFileURL = "smp://tacsatmini.csv?5ezvFfBOLqa2CUPC0velBUnqe0zlyBOiHB8b4B4yi0tsfi7ohCndPEZuRB/t7SXwAms8bk8KwvyHVLeQ2bBnUSnXP87yjTYTEFaZxxzNE/tmBefs5CNO3iRTeJGE8NDJ1bwVGRS//+4QELLbyLZ/GesZiduaN+bqrNOs/9/AGgA3Pq24H+aXe5suWD31Sxwu";
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String defaultInputFile = "tacsat.csv";
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String defaultOutputFile = "tacsat_interpolated.csv";
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LinkedHashMap<String, String> inputParameters = new LinkedHashMap<String, String>();
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inputParameters.put("interval", "120");
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inputParameters.put("margin", "10");
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inputParameters.put("res", "100");
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inputParameters.put("method", "\"cHs\"");
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inputParameters.put("fm", "0.5");
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inputParameters.put("distscale", "20");
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inputParameters.put("sigline", "0.2");
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inputParameters.put("minspeedThr", "2");
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inputParameters.put("maxspeedThr", "6");
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inputParameters.put("st", "c(minspeedThr,maxspeedThr)");
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inputParameters.put("headingAdjustment", "0");
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inputParameters.put("fast", "TRUE");
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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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}
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*/
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}
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