278 lines
12 KiB
Java
278 lines
12 KiB
Java
package org.gcube.dataanalysis.executor.rscripts.generic;
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import java.io.File;
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import java.io.FileWriter;
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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.apache.commons.io.FileUtils;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.contentmanagement.lexicalmatcher.utils.FileTools;
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import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
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import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
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import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
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import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalInfraAlgorithm;
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import org.gcube.dataanalysis.ecoengine.utils.ZipTools;
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import org.gcube.dataanalysis.executor.util.LocalRScriptsManager;
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import org.gcube.dataanalysis.executor.util.StorageUtils;
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public abstract class GenericRScript extends StandardLocalInfraAlgorithm {
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// FIXED part
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protected HashMap<String, String> outputValues = new HashMap<String, String>();
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protected LinkedHashMap<String, StatisticalType> output = new LinkedHashMap<String, StatisticalType>();
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LocalRScriptsManager scriptmanager;
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@Override
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public void shutdown() {
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// in the case of forced shutdown, stop the R process
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if (scriptmanager != null)
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scriptmanager.stop();
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System.gc();
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}
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@Override
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public void init() throws Exception {
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AnalysisLogger.getLogger().debug("Initializing " + this.getClass().getCanonicalName());
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initVariables();
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}
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@Override
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protected void process() throws Exception {
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boolean deletefiles = true; // for test only
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String Rlog = null;
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// init status
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status = 0;
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try {
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// instantiate the R Script executor
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scriptmanager = new LocalRScriptsManager();
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// download and unzip the script in a controlled folder
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AnalysisLogger.getLogger().debug("Starting script");
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File localPackage = new File(config.getConfigPath(), "package" + UUID.randomUUID() + ".zip");
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AnalysisLogger.getLogger().debug("Downloading package " + packageURL + "as: " + localPackage.getAbsolutePath());
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StorageUtils.downloadInputFile(packageURL, localPackage.getAbsolutePath(), true);
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AnalysisLogger.getLogger().debug("Generating sandbox folder");
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File folder = new File(config.getConfigPath(), "rscr_" + UUID.randomUUID());
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boolean mkdir = folder.mkdir();
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AnalysisLogger.getLogger().debug("Sandbox " + folder.getAbsolutePath() + " generated: " + mkdir);
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AnalysisLogger.getLogger().debug("Unzipping package into " + folder.getAbsolutePath());
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ZipTools.unZip(localPackage.getAbsolutePath(), folder.getAbsolutePath());
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localPackage.delete();
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// File folder = new File("C:/Users/coro/Desktop/WorkFolder/Workspace/EcologicalEngineSmartExecutor/./cfg/rscr_7d329495-b048-4ce0-8bcc-bd74966db56d/");
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AnalysisLogger.getLogger().debug("Analysing inputs");
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// distinguish the environmental variables and the input variables
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HashMap<String, String> inputParameters = new LinkedHashMap<String, String>();
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int i = 0;
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List<StatisticalType> inputs = getInputParameters();
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for (String input : inputvariables) {
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String value = config.getParam(input);
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if (value == null)
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value = "";
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String defaultValue = inputs.get(i).getDefaultValue();
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defaultValue = defaultValue.replace("(", "\\(").replace(")", "\\)").replace("[", "\\[").replace("]", "\\]").replace("|", "\\|").replace(".", "\\.").replace("?", "\\?").replace("*", "\\*").replace("+", "\\+").replace("{", "\\{").replace("}", "\\}");
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// inputParameters.put(defaultValue, value);
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String punct = "[ \";]*";
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String regexp = punct + input + punct + "(<-|=)" + punct + defaultValue + punct + ".*";
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boolean string = true;
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try {
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Double.parseDouble(value);
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string = false;
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} catch (Exception ee) {
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}
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String line = input + "=" + value;
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if (string && !value.equals("T") && !value.equalsIgnoreCase("true") && !value.equalsIgnoreCase("false") && !value.equalsIgnoreCase("F"))
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line = input + "=\"" + value + "\"";
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inputParameters.put(regexp, line);
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i++;
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}
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AnalysisLogger.getLogger().debug("Inputs: " + inputParameters.toString());
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AnalysisLogger.getLogger().debug("Analysing environmental variables");
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HashMap<String, String> environmentalParameters = new LinkedHashMap<String, String>();
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for (String environment : environmentalvariables) {
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String value = config.getParam(environment);
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environmentalParameters.put(environment, value);
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}
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AnalysisLogger.getLogger().debug("Environmental: " + environmentalParameters.toString());
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AnalysisLogger.getLogger().debug("Analysing output variables");
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HashMap<String, String> outputParameters = new LinkedHashMap<String, String>();
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for (String output : outputvariables) {
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outputParameters.put(output, "");
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}
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AnalysisLogger.getLogger().debug("Output: " + outputParameters.toString());
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AnalysisLogger.getLogger().debug("Main script: " + mainScriptName);
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AnalysisLogger.getLogger().debug("Processing main script name");
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// build the script name
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String scriptName = mainScriptName;
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String scriptSubfolder = "";
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int lioSlash = scriptName.lastIndexOf("/");
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if (lioSlash > -1) {
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scriptSubfolder = scriptName.substring(0, lioSlash);
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scriptName = scriptName.substring(lioSlash + 1);
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}
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scriptSubfolder = new File(folder.getAbsoluteFile(), scriptSubfolder).getAbsolutePath();
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AnalysisLogger.getLogger().debug("Main script name: " + scriptName);
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AnalysisLogger.getLogger().debug("Main script folder: " + scriptSubfolder);
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boolean scriptMustReturnAFile = false;
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boolean uploadScriptOnTheInfrastructureWorkspace = false;
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status = 10;
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AnalysisLogger.getLogger().debug("Executing the script...");
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// execute the script in multi-user mode
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Rlog = scriptmanager.executeRScript(config, scriptName, null, environmentalParameters, outputParameters, null, null, inputParameters, scriptMustReturnAFile, uploadScriptOnTheInfrastructureWorkspace, deletefiles, scriptSubfolder);
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AnalysisLogger.getLogger().debug("..execution finished!");
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// get the output: one file should have been produced for each output
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AnalysisLogger.getLogger().debug("Getting output");
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for (String output : outputvariables) {
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File outPath = new File(scriptSubfolder, output);
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AnalysisLogger.getLogger().debug("Output " + output + " - loading respective file from " + outPath.getAbsolutePath());
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AnalysisLogger.getLogger().debug("File exists? " + outPath.exists());
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String fileContent = FileTools.loadString(outPath.getAbsolutePath(), "UTF-8");
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fileContent = analyseContent(fileContent, scriptSubfolder);
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AnalysisLogger.getLogger().debug("Retrieved output content: " + output + ": " + fileContent);
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outputValues.put(output, fileContent);
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}
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// delete the script folder
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try {
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if (deletefiles) {
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AnalysisLogger.getLogger().debug("Deleting sandbox folder");
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FileUtils.cleanDirectory(folder);
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FileUtils.deleteDirectory(folder);
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AnalysisLogger.getLogger().debug("Folder " + folder.getAbsolutePath() + " deleted");
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}
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} catch (Exception e) {
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AnalysisLogger.getLogger().warn("Could not delete sandbox folder {} ",folder.getAbsolutePath(),e);
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}
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if (Rlog != null) {
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File logFile = saveLogFile(Rlog);
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output.put("Log", new PrimitiveType(File.class.getName(), logFile, PrimitiveTypes.FILE, "LogFile", "Log of the computation"));
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}
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} catch (Exception e) {
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if (Rlog != null) {
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String httpurl = generateRemoteLogFile(Rlog);
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String message = "Logs of the script can be found at "+httpurl;
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e = new Exception(message);
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}
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throw e;
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} finally {
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AnalysisLogger.getLogger().debug("Computation finished.");
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status = 100;
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}
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}
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protected File saveLogFile(String Rlog) throws Exception {
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String uuid = "" + UUID.randomUUID();
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AnalysisLogger.getLogger().debug("Writing the logs of the execution");
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File logfile = new File(config.getPersistencePath(), "RLOG" + uuid + ".txt");
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FileWriter fw = new FileWriter(logfile);
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fw.write(Rlog);
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fw.close();
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AnalysisLogger.getLogger().debug("Written in " + logfile);
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return logfile;
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}
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protected String generateRemoteLogFile(String Rlog) throws Exception {
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String uuid = "" + UUID.randomUUID();
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AnalysisLogger.getLogger().debug("Writing the logs of the execution");
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File logfile = new File(config.getPersistencePath(), "RLOG" + uuid + ".txt");
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FileWriter fw = new FileWriter(logfile);
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fw.write(Rlog);
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fw.close();
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AnalysisLogger.getLogger().debug("Written in " + logfile);
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String httpurl = StorageUtils.uploadFilesOnStorage(config.getGcubeScope(), config.getParam("ServiceUserName"), logfile.getParent(), "/ScriptLogs/" + uuid + "/", logfile.getName(),true);
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AnalysisLogger.getLogger().debug("Uploaded on storage: " + httpurl);
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// String httpurl = url.replace("smp:", "http:");
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/*
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if (config.getGcubeScope().startsWith("/gcube"))
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httpurl = "http://data-d.d4science.org/uri-resolver/smp?smp-uri=" + url + "&fileName=" + logfile.getName() ;
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else
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httpurl = "http://data.d4science.org/uri-resolver/smp?smp-uri=" + url + "&fileName=" + logfile.getName() ;
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*/
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AnalysisLogger.getLogger().debug("Deleting log file and returning " + httpurl);
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logfile.delete();
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// httpurl = URLEncoder.encode(httpurl, "UTF-8");
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return httpurl;
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}
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protected String analyseContent(String filecontent, String scriptfolder) throws Exception {
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AnalysisLogger.getLogger().debug("Analysing file content");
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String[] rows = filecontent.split(System.lineSeparator());
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List<String> files = new ArrayList<String>();
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for (String row : rows) {
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AnalysisLogger.getLogger().debug("Analysing -> " + row);
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if (row != null) {
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row = row.replace("\"", "");
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File rowFile = new File(row.trim());
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AnalysisLogger.getLogger().debug("Checking row file-> " + rowFile.getAbsolutePath());
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if (!rowFile.exists()) {
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rowFile = new File(scriptfolder, row.trim());
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AnalysisLogger.getLogger().debug("File does not exist - checking complete row file-> " + rowFile.getAbsolutePath());
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}
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if (rowFile.exists()) {
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String preparedFile = new File(config.getConfigPath(), rowFile.getName()).getAbsolutePath();
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AnalysisLogger.getLogger().debug("Copying " + rowFile.getAbsolutePath() + " to " + preparedFile);
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try{
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org.gcube.dataanalysis.executor.rscripts.generic.FileUtils.moveFileToDirectory(rowFile, new File(config.getConfigPath()), false);
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files.add(preparedFile);
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}catch(Exception e){
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AnalysisLogger.getLogger().error("error in moving file {} to {}",rowFile.getAbsolutePath(),preparedFile,e);
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throw e;
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}
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break;
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} else
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AnalysisLogger.getLogger().debug("Checking row file does not exist - treating as a String");
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}
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}
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if (files.size() > 0) {
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AnalysisLogger.getLogger().debug("A File was recognized as output");
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return files.get(0);
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} else {
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AnalysisLogger.getLogger().debug("A String was recognized as output");
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return filecontent;
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}
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}
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// DYNAMIC part
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protected String mainScriptName = "";
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protected String packageURL = "";
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protected List<String> environmentalvariables = new ArrayList<String>();
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protected List<String> inputvariables = new ArrayList<String>();
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protected List<String> outputvariables = new ArrayList<String>();
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protected void initVariables() {
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}
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@Override
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protected void setInputParameters() {
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}
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@Override
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public StatisticalType getOutput() {
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return null;
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}
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}
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