Gianpaolo Coro 2016-01-10 18:52:08 +00:00
parent 1e8f6f3e3d
commit 78d75bca07
1 changed files with 305 additions and 0 deletions

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package org.gcube.dataanalysis.executor.util;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.util.ArrayList;
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;
public class LocalRScriptsManager {
public float status = 0;
public String currentOutputURL;
Process process;
public String getCurrentOutputURL() {
return currentOutputURL;
}
public void setCurrentOutputURL(String currentOutputURL) {
this.currentOutputURL = currentOutputURL;
}
public String currentOutputFileName;
public String getCurrentOutputFileName() {
return currentOutputFileName;
}
public void setCurrentOutputFileName(String currentOutputFileName) {
this.currentOutputFileName = currentOutputFileName;
}
public float getStatus() {
return status;
}
public void setStatus(float status) {
this.status = status;
}
public static void substituteStringInFile(String file, String newFile, String s, String sub) throws Exception {
BufferedReader br = new BufferedReader(new FileReader(new File(file)));
BufferedWriter bw = new BufferedWriter(new FileWriter(new File(newFile)));
String line = br.readLine();
while (line != null) {
int idx = line.indexOf(s);
if (idx >= 0) {
line = line.replace(s, sub);
}
bw.write(line + "\n");
line = br.readLine();
}
br.close();
bw.close();
}
public static void printRConsole(Process process) {
try {
BufferedReader br = new BufferedReader(new InputStreamReader(process.getInputStream()));
String line = br.readLine();
StringBuffer sb = new StringBuffer();
while (line != null) {
line = br.readLine();
sb.append(line + "\n");
}
AnalysisLogger.getLogger().debug(sb);
AnalysisLogger.getLogger().debug("---ERRORS---");
br = new BufferedReader(new InputStreamReader(process.getErrorStream()));
line = br.readLine();
sb = new StringBuffer();
while (line != null) {
line = br.readLine();
sb.append(line + "\n");
}
AnalysisLogger.getLogger().debug(sb);
AnalysisLogger.getLogger().debug("---END OF ERRORS---");
} catch (Exception e) {
AnalysisLogger.getLogger().debug("---END BY PROCESS INTERRUPTION---");
}
}
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 {
executeRScript(config, scriptName, inputFileURL, inputParameters, null, defaultInputFile, defaultOutputFile, codeInjections, mustReturnAFile, uploadOutputOnStorage, true, sandboxFolder);
}
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 {
executeRScript(config, scriptName, inputFileURL, inputParameters, outputParameters, defaultInputFile, defaultOutputFile, codeInjections, mustReturnAFile, uploadOutputOnStorage, true, sandboxFolder);
}
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 {
executeRScript(config, scriptName, inputFileURL, inputParameters, null, defaultInputFile, defaultOutputFile, codeInjections, mustReturnAFile, uploadOutputOnStorage, deletefiles, sandboxFolder);
}
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 {
List<String> tempfiles = new ArrayList<String>();
try {
status = 0;
String scriptPath = new File(sandboxFolder, scriptName).getAbsolutePath();
// String originalScriptPath = scriptPath;
String preparedScriptPath = null;
String owner = config.getParam("ServiceUserName");
if (owner == null)
owner = "ecological.engine";
String scope = config.getGcubeScope();
if (scope == null)
scope = ScopeProvider.instance.get();
AnalysisLogger.getLogger().debug("Current User: " + owner);
AnalysisLogger.getLogger().debug("Current Scope: " + scope);
AnalysisLogger.getLogger().debug("Sandbox Folder: " + sandboxFolder);
AnalysisLogger.getLogger().debug("Script : " + scriptPath);
AnalysisLogger.getLogger().debug("Prepared Script : " + preparedScriptPath);
try {
OSCommand.ExecuteGetLine("ls", null);
OSCommand.ExecuteGetLine("pwd", null);
OSCommand.ExecuteGetLine("chmod +x * | whoami", null);
} catch (Throwable e) {
AnalysisLogger.getLogger().debug("Cannot execute SO commands");
}
if (codeInjections != null) {
for (String toSubstitute : codeInjections.keySet()) {
String substitution = codeInjections.get(toSubstitute);
AnalysisLogger.getLogger().debug("Substituting : " + toSubstitute + " with " + substitution);
preparedScriptPath = new File(sandboxFolder, UUID.randomUUID() + scriptName).getAbsolutePath();
substituteStringInFile(scriptPath, preparedScriptPath, toSubstitute, substitution);
AnalysisLogger.getLogger().debug("New Script name: " + preparedScriptPath+" exists: "+new File(preparedScriptPath).exists());
tempfiles.add(preparedScriptPath);
scriptPath = preparedScriptPath;
}
}
if (defaultInputFile!=null){
String newInputFile = new File(sandboxFolder, UUID.randomUUID() + defaultInputFile).getAbsolutePath().replace("\\", "/");
tempfiles.add(newInputFile);
AnalysisLogger.getLogger().debug("New Input File is " + newInputFile);
if (inputFileURL.trim().length() > 0) {
AnalysisLogger.getLogger().debug("Substituting standard Input");
preparedScriptPath = new File(sandboxFolder, UUID.randomUUID() + scriptName).getAbsolutePath();
substituteStringInFile(scriptPath, preparedScriptPath, defaultInputFile, newInputFile);
} else {
if ((preparedScriptPath==null) || (preparedScriptPath.trim().length()==0))
preparedScriptPath = new File(sandboxFolder, scriptName).getAbsolutePath();
}
AnalysisLogger.getLogger().debug("Creating local file from remote file");
if (inputFileURL.startsWith("http:") || inputFileURL.startsWith("smp:")) {
StorageUtils.downloadInputFile(inputFileURL, newInputFile);
} else if (inputFileURL.trim().length() > 0) {
OSCommand.FileCopy(inputFileURL, newInputFile);
}
tempfiles.add(preparedScriptPath);
scriptPath = preparedScriptPath;
}
String newOutputFile = UUID.randomUUID().toString() + defaultOutputFile;
String newOutputFilePath = new File(sandboxFolder, newOutputFile).getAbsolutePath().replace("\\", "/");
if (defaultOutputFile!=null){
int extension = defaultOutputFile.lastIndexOf(".");
if (extension > 0)
newOutputFile = defaultOutputFile.substring(0, extension) + "_" + UUID.randomUUID().toString() + "." + defaultOutputFile.substring(extension + 1);
newOutputFilePath = new File(sandboxFolder, newOutputFile).getAbsolutePath().replace("\\", "/");
AnalysisLogger.getLogger().debug("New Output File is " + newOutputFilePath);
AnalysisLogger.getLogger().debug("Substituting standard Output");
preparedScriptPath = new File(sandboxFolder, UUID.randomUUID() + scriptName).getAbsolutePath();
substituteStringInFile(scriptPath, preparedScriptPath, defaultOutputFile, newOutputFilePath);
tempfiles.add(preparedScriptPath);
scriptPath = preparedScriptPath;
}
AnalysisLogger.getLogger().debug("Executing R script " + scriptPath);
status = 10;
// run the R code
String scriptdir = new File(scriptPath).getParent().replace("\\", "/");
process = Runtime.getRuntime().exec("R --no-save\n",null,new File(scriptdir));
BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(process.getOutputStream()));
//set the working directory to the one of the script
bw.write("setwd(\""+scriptdir+"\")\n");
for (String inputparam : inputParameters.keySet()) {
String value = inputParameters.get(inputparam);
bw.write(inputparam + "<-" + value + "\n");
}
bw.write("source('" + scriptPath.replace("\\", "/") + "')\n");
// bw.write("source('" + originalScriptPath.replace("\\", "/") + "')\n");
if (outputParameters!=null){
for (String outputparam : outputParameters.keySet()) {
bw.write("paste(\"out->\","+outputparam+")"+ "\n");
bw.write("write.csv("+outputparam+",file=\""+new File(sandboxFolder,outputparam).getAbsolutePath().replace("\\", "/")+"\",row.names=FALSE,append=F,fileEncoding=\"UTF-8\",eol = \"\\n\")"+ "\n");
}
}
bw.write("q()\n");
bw.close();
printRConsole(process);
process.destroy();
if ((new File(newOutputFilePath)).exists()) {
if (uploadOutputOnStorage) {
AnalysisLogger.getLogger().debug("Found output file ... saving on the workspace");
String outputURL = StorageUtils.uploadFilesOnStorage(scope, owner, sandboxFolder, newOutputFile);
currentOutputURL = outputURL;
AnalysisLogger.getLogger().debug("Output URL is " + outputURL);
}
currentOutputFileName = newOutputFilePath;
AnalysisLogger.getLogger().debug("Output File is " + currentOutputFileName);
} else if (!mustReturnAFile) {
AnalysisLogger.getLogger().debug("No file detected as output");
currentOutputFileName = null;
currentOutputURL = null;
} else
throw new Exception("The script did not return an output - an error occurred");
AnalysisLogger.getLogger().debug("The procedure was successful");
status = 100f;
} catch (Exception e) {
e.printStackTrace();
AnalysisLogger.getLogger().debug("The R Script generated an error! " + e.getLocalizedMessage());
throw e;
} finally {
if (deletefiles) {
AnalysisLogger.getLogger().debug("Deleting temp files");
for (String file : tempfiles) {
boolean deleted = new File(file).delete();
AnalysisLogger.getLogger().debug("Deleting " + file + " " + deleted);
}
AnalysisLogger.getLogger().debug("Done: Deleted temp files");
}
}
}
public void stop() {
if (process != null) {
try {
process.destroy();
} catch (Exception e) {
}
}
}
public static void main1(String[] args) throws Exception {
String url = StorageUtils.uploadFilesOnStorage("/gcube/devsec/devVRE", "ecological.engine", "C:\\Users\\coro\\Documents\\", "tacsatmini.csv");
System.out.println(url);
}
public static void main(String[] args) throws Exception {
LocalRScriptsManager scriptmanager = new LocalRScriptsManager();
AnalysisLogger.setLogger("./cfg/" + AlgorithmConfiguration.defaultLoggerFile);
AlgorithmConfiguration config = new AlgorithmConfiguration();
config.setGcubeScope("/gcube/devsec/devVRE");
config.setPersistencePath("./PARALLEL_PROCESSING");
String scriptName = "interpolateTacsat.r";
String inputFileURL = "smp://tacsatmini.csv?5ezvFfBOLqa2CUPC0velBUnqe0zlyBOiHB8b4B4yi0tsfi7ohCndPEZuRB/t7SXwAms8bk8KwvyHVLeQ2bBnUSnXP87yjTYTEFaZxxzNE/tmBefs5CNO3iRTeJGE8NDJ1bwVGRS//+4QELLbyLZ/GesZiduaN+bqrNOs/9/AGgA3Pq24H+aXe5suWD31Sxwu";
String defaultInputFile = "tacsat.csv";
String defaultOutputFile = "tacsat_interpolated.csv";
LinkedHashMap<String, String> inputParameters = new LinkedHashMap<String, String>();
inputParameters.put("interval", "120");
inputParameters.put("margin", "10");
inputParameters.put("res", "100");
inputParameters.put("method", "\"cHs\"");
inputParameters.put("fm", "0.5");
inputParameters.put("distscale", "20");
inputParameters.put("sigline", "0.2");
inputParameters.put("minspeedThr", "2");
inputParameters.put("maxspeedThr", "6");
inputParameters.put("st", "c(minspeedThr,maxspeedThr)");
inputParameters.put("headingAdjustment", "0");
inputParameters.put("fast", "TRUE");
inputParameters.put("npoints", "10");
inputParameters.put("equalDist", "TRUE");
scriptmanager.executeRScript(config, scriptName, inputFileURL, inputParameters, defaultInputFile, defaultOutputFile, null, true, true,"./");
}
}