package org.gcube.dataanalysis.executor.rscripts.generic;

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.UUID;

import org.apache.commons.io.FileUtils;
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
import org.gcube.contentmanagement.lexicalmatcher.utils.FileTools;
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm;
import org.gcube.dataanalysis.ecoengine.utils.ZipTools;
import org.gcube.dataanalysis.executor.scripts.OSCommand;
import org.gcube.dataanalysis.executor.util.LocalRScriptsManager;
import org.gcube.dataanalysis.executor.util.RScriptsManager;
import org.gcube.dataanalysis.executor.util.StorageUtils;

public abstract class GenericRScript extends StandardLocalExternalAlgorithm {

	//FIXED part
	protected HashMap<String,String> outputValues=new HashMap<String,String>();
	protected LinkedHashMap<String, StatisticalType> output = new LinkedHashMap<String, StatisticalType> ();
	LocalRScriptsManager scriptmanager;
	
	@Override
	public void shutdown() {
		//in the case of forced shutdown, stop the R process
		if (scriptmanager!=null)
			scriptmanager.stop();
		System.gc();
	}
	@Override
	public void init() throws Exception {
		AnalysisLogger.getLogger().debug("Initializing "+this.getClass().getCanonicalName());
		initVariables();
	}
	
	@Override
	protected void process() throws Exception {
		//init status
		status = 0;
		//instantiate the R Script executor
		scriptmanager = new LocalRScriptsManager();
		//download and unzip the script in a controlled folder
		AnalysisLogger.getLogger().debug("Starting script");
		
		File localPackage = new File(config.getConfigPath(),"package"+UUID.randomUUID()+".zip");
		AnalysisLogger.getLogger().debug("Downloading package "+packageURL+"as: "+localPackage.getAbsolutePath());
		StorageUtils.downloadInputFile(packageURL, localPackage.getAbsolutePath(),true);
		AnalysisLogger.getLogger().debug("Generating sandbox folder");
		File folder = new File(config.getConfigPath(),"rscr_"+UUID.randomUUID());
		boolean mkdir = folder.mkdir();
		AnalysisLogger.getLogger().debug("Sandbox "+folder.getAbsolutePath()+" generated: "+mkdir);
		AnalysisLogger.getLogger().debug("Unzipping package into "+folder.getAbsolutePath());
		ZipTools.unZip(localPackage.getAbsolutePath(), folder.getAbsolutePath());
		localPackage.delete();
	
		
		//File folder = new File("C:/Users/coro/Desktop/WorkFolder/Workspace/EcologicalEngineSmartExecutor/./cfg/rscr_7d329495-b048-4ce0-8bcc-bd74966db56d/");
		 
		AnalysisLogger.getLogger().debug("Analysing inputs");
		//distinguish the environmental variables and the input variables
		HashMap<String,String> inputParameters = new LinkedHashMap<String, String>();
		int i=0;
		List<StatisticalType>inputs = getInputParameters();
		for (String input:inputvariables){
			String value = config.getParam(input);
			String defaultValue = inputs.get(i).getDefaultValue();
			inputParameters.put(defaultValue, value);
			i++;
		}
		AnalysisLogger.getLogger().debug("Inputs: "+inputParameters.toString());
		AnalysisLogger.getLogger().debug("Analysing environmental variables");
		HashMap<String,String> environmentalParameters = new LinkedHashMap<String, String>();
		for (String environment:environmentalvariables){
			String value = config.getParam(environment);
			environmentalParameters.put(environment, value);
		}
		AnalysisLogger.getLogger().debug("Environmental: "+environmentalParameters.toString());
		AnalysisLogger.getLogger().debug("Analysing output variables");
		HashMap<String,String> outputParameters = new LinkedHashMap<String, String>();
		for (String output:outputvariables){
			outputParameters.put(output, "");
		}
		AnalysisLogger.getLogger().debug("Output: "+outputParameters.toString());
		
		AnalysisLogger.getLogger().debug("Main script: "+mainScriptName);
		AnalysisLogger.getLogger().debug("Processing main script name");
		//build the script name
		String scriptName = mainScriptName;
		String scriptSubfolder = "";
		int lioSlash = scriptName.lastIndexOf("/");
		if (lioSlash>-1){
			scriptSubfolder = scriptName.substring(0,lioSlash);
			scriptName = scriptName.substring(lioSlash+1);
		}
		scriptSubfolder = new File (folder.getAbsoluteFile(),scriptSubfolder).getAbsolutePath();
		AnalysisLogger.getLogger().debug("Main script name: "+scriptName);
		AnalysisLogger.getLogger().debug("Main script folder: "+scriptSubfolder);
		
		boolean scriptMustReturnAFile = false;
		boolean uploadScriptOnTheInfrastructureWorkspace = false;
		status = 10;
		AnalysisLogger.getLogger().debug("Executing the script...");
		//execute the script in multi-user mode
		scriptmanager.executeRScript(config, scriptName, null, environmentalParameters, outputParameters, null, null,inputParameters, scriptMustReturnAFile,uploadScriptOnTheInfrastructureWorkspace, true, scriptSubfolder);
		AnalysisLogger.getLogger().debug("..execution finished!");
		//get the output: one file should have been produced for each output
		AnalysisLogger.getLogger().debug("Getting output");
		for (String output:outputvariables){
			File outPath = new File(scriptSubfolder,output);
			AnalysisLogger.getLogger().debug("Output "+output +" - loading respective file from "+outPath.getAbsolutePath());
			AnalysisLogger.getLogger().debug("File exists? "+outPath.exists());
			String fileContent = FileTools.loadString(outPath.getAbsolutePath(), "UTF-8");
			fileContent=analyseContent(fileContent);
			AnalysisLogger.getLogger().debug("Retrieved output content: "+output+": "+fileContent);
			outputValues.put(output, fileContent);
		}

		//delete the script folder
		AnalysisLogger.getLogger().debug("Deleting sandbox folder");
		try{
			FileUtils.cleanDirectory(folder);
			FileUtils.deleteDirectory(folder);
			AnalysisLogger.getLogger().debug("Folder "+folder.getAbsolutePath()+ " deleted");
		}catch(Exception e){
			AnalysisLogger.getLogger().debug(e);
			AnalysisLogger.getLogger().debug("Could not delete sandbox folder "+folder.getAbsolutePath());
		}
		AnalysisLogger.getLogger().debug("Computation finished.");
		status = 100;
	}
	
	protected String analyseContent(String filecontent) throws Exception{
		String [] rows = filecontent.split("\n");
		List<String> files = new ArrayList<String>();
		for (String row:rows){
			if (row!=null)
				row = row.replace("\"", "");
			if ((new File(row)).exists()){
				String preparedFile = new File(config.getConfigPath(),new File(row).getName()).getAbsolutePath();
				AnalysisLogger.getLogger().debug("Copying "+row+" to "+preparedFile);
					FileUtils.moveFileToDirectory(new File(row), new File(config.getConfigPath()), false);
					files.add(preparedFile);
				
				break;
			}	
		}
		
		if (files.size()>0)
			return files.get(0);
		else
			return filecontent;
	}
	//DYNAMIC part
	protected String mainScriptName="";
	protected String packageURL="";
	
	protected List<String> environmentalvariables = new ArrayList<String>();
	protected List<String> inputvariables= new ArrayList<String>();
	protected List<String> outputvariables= new ArrayList<String>();
	
	
	protected void initVariables(){
		
	}
	
	@Override
	protected void setInputParameters() {
	}
	
	@Override
	public StatisticalType getOutput() {
		return null;
	}

}