git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineSmartExecutor@113923 82a268e6-3cf1-43bd-a215-b396298e98cf
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package org.gcube.dataanalysis.executor.nodes.algorithms;
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import java.io.File;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.List;
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import java.util.UUID;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.ecoengine.configuration.ALG_PROPS;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
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import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveTypesList;
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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.ActorNode;
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import org.gcube.dataanalysis.ecoengine.utils.IOHelper;
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import org.gcube.dataanalysis.ecoengine.utils.Transformations;
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import org.gcube.dataanalysis.executor.scripts.OSCommand;
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import org.gcube.dataanalysis.executor.util.RScriptsManager;
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import org.gcube.dataanalysis.executor.util.StorageUtils;
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public class FAOMSY extends ActorNode {
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public int count;
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public float status = 0;
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@Override
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public ALG_PROPS[] getProperties() {
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ALG_PROPS[] p = { ALG_PROPS.PHENOMENON_VS_PARALLEL_PHENOMENON };
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return p;
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}
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@Override
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public String getName() {
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return "FAOMSY";
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}
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@Override
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public String getDescription() {
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return "An algorithm to estimate the Maximum Sustainable Yield from a catch statistic by FAO.";
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}
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static String stocksFile = "StocksFile";
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static String processOutput= "ProcessOutput";
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static String nonProcessedOutput= "NonProcessedOutput";
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static String scriptName = "CatchMSY_Dec2014.R";
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@Override
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public List<StatisticalType> getInputParameters() {
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List<StatisticalType> parameters = new ArrayList<StatisticalType>();
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IOHelper.addStringInput(parameters, stocksFile, "Http link to a file containing catch statistics for a group of species. Example: http://goo.gl/g6YtVx", "");
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return parameters;
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}
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@Override
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public StatisticalType getOutput() {
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File outfile = new File(config.getPersistencePath(),config.getParam(processOutput));
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File outfile2 = new File(config.getPersistencePath(),config.getParam(nonProcessedOutput));
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PrimitiveTypesList list = new PrimitiveTypesList(File.class.getName(), PrimitiveTypes.FILE, "OutputFiles", "Textual output files - processed and non-processed species",false);
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if (outfile.exists()){
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PrimitiveType o = new PrimitiveType(File.class.getName(), outfile, PrimitiveTypes.FILE, "ProcessedSpecies", "Output file");
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list.add(o);
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}
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if (outfile2.exists()){
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PrimitiveType o2 = new PrimitiveType(File.class.getName(), outfile2, PrimitiveTypes.FILE, "NonProcessedSpecies", "Output file");
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list.add(o2);
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}
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return list;
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}
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@Override
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public void initSingleNode(AlgorithmConfiguration config) {
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}
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@Override
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public float getInternalStatus() {
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return status;
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}
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AlgorithmConfiguration config;
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@Override
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public int executeNode(int leftStartIndex, int numberOfLeftElementsToProcess, int rightStartIndex, int numberOfRightElementsToProcess, boolean duplicate, String sandboxFolder, String nodeConfigurationFileObject, String logfileNameToProduce) {
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try {
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status = 0;
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config = Transformations.restoreConfig(nodeConfigurationFileObject);
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String outputFile = config.getParam(processOutput)+"_part"+rightStartIndex;
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String nonprocessedoutputFile = config.getParam(nonProcessedOutput)+"_part"+rightStartIndex;
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AnalysisLogger.getLogger().info("FAOMSY ranges: "+" Li:"+leftStartIndex+" NLi:"+leftStartIndex+" Ri:"+rightStartIndex+" NRi:"+numberOfRightElementsToProcess);
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AnalysisLogger.getLogger().info("FAOMSY expected output "+outputFile);
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File filestock=new File(sandboxFolder,"D20_1.csv");
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StorageUtils.downloadInputFile(config.getParam(stocksFile), filestock.getAbsolutePath());
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AnalysisLogger.getLogger().debug("Check fileStocks: "+filestock.getAbsolutePath()+" "+filestock.exists());
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File filestocksub=new File(sandboxFolder,"D20.csv");
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StorageUtils.FileSubset(filestock, filestocksub, rightStartIndex, numberOfRightElementsToProcess, true);
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RScriptsManager scriptmanager = new RScriptsManager();
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HashMap<String,String> codeinj = new HashMap<String,String>();
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config.setConfigPath("./");
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scriptmanager.executeRScript(config, scriptName, "", new HashMap<String,String>(), "", "CatchMSY_Output.csv", codeinj, false,false,false);
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AnalysisLogger.getLogger().info("FAOMSY The script has finished");
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String outputFileName = "";
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//manage the fact that the outputfile could even not exist
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try{outputFileName = scriptmanager.getCurrentOutputFileName();}catch(Exception e){
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AnalysisLogger.getLogger().info("FAOMSY Could not get curent output file");
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}
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String optionalFileOutputName = "NonProcessedSpecies.csv";
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if (outputFileName!=null && outputFileName.length()>0 && new File(outputFileName).exists()){
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AnalysisLogger.getLogger().info("FAOMSY Main file exists!");
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outputFileName = scriptmanager.getCurrentOutputFileName();
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String outputFilePath = new File(sandboxFolder,outputFile).getAbsolutePath();
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AnalysisLogger.getLogger().info("FAOMSY writing output file in path "+outputFilePath);
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OSCommand.FileCopy(outputFileName,outputFilePath);
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AnalysisLogger.getLogger().info("FAOMSY uploading output file "+outputFile);
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StorageUtils.uploadFilesOnStorage(config.getGcubeScope(), config.getParam("ServiceUserName"), sandboxFolder,outputFile);
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}
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if (new File(optionalFileOutputName).exists()){
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AnalysisLogger.getLogger().info("FAOMSY Optional file exists!");
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OSCommand.FileCopy(optionalFileOutputName,nonprocessedoutputFile);
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AnalysisLogger.getLogger().info("FAOMSY uploading output file "+nonprocessedoutputFile);
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//check only
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// String file = FileTools.loadString(nonprocessedoutputFile, "UTF-8");
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// AnalysisLogger.getLogger().info("FAOMSY File check"+file);
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StorageUtils.uploadFilesOnStorage(config.getGcubeScope(), config.getParam("ServiceUserName"), sandboxFolder,nonprocessedoutputFile);
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}
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AnalysisLogger.getLogger().info("FAOMSY Finished");
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}catch(Exception e){
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e.printStackTrace();
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}
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return 0;
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}
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@Override
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public void setup(AlgorithmConfiguration config) throws Exception {
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this.config = config;
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AnalysisLogger.getLogger().info("FAOMSY process is initialized");
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String uuid = (UUID.randomUUID()+".txt").replace("-", "");
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config.setParam(processOutput, "FAOMSY_"+"output_"+uuid);
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config.setParam(nonProcessedOutput, "FAOMSY_nonprocessed_"+"output_"+uuid);
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File tempfile = new File(config.getPersistencePath(),"FAOMSY_input_"+(UUID.randomUUID()+".csv").replace("-", ""));
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StorageUtils.downloadInputFile(config.getParam(stocksFile), tempfile.getAbsolutePath());
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nstocks = StorageUtils.calcFileRows(tempfile, true);
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AnalysisLogger.getLogger().info("FAOMSY Found "+nstocks+" stocks!");
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if (nstocks==0)
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throw new Exception("Error in FAOMSY: No stocks to process found in the file "+config.getParam(stocksFile));
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}
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int nstocks = 0;
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@Override
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public int getNumberOfRightElements() {
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return nstocks;
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}
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@Override
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public int getNumberOfLeftElements() {
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return 1;
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}
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@Override
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public void stop() {
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AnalysisLogger.getLogger().info("CMSY process stopped");
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}
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boolean haspostprocessed = false;
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public void assembleFiles(String outputFileName) throws Exception{
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//try downloading all the files
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List<String> fileslist = new ArrayList<String>();
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for (int i=0;i<=nstocks;i++){
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String filename = outputFileName+"_part"+i;
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try{
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StorageUtils.downloadFilefromStorage(config.getGcubeScope(), config.getParam("ServiceUserName"), config.getPersistencePath(), filename);
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AnalysisLogger.getLogger().debug("FAOMSY - Saved from Storage: "+filename);
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fileslist.add(filename);
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}catch(Exception e){
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AnalysisLogger.getLogger().debug("FAOMSY - Did not save file from Storage: "+filename);
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}
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}
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AnalysisLogger.getLogger().debug("FAOMSY - Merging files in "+outputFileName);
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if (fileslist.size()>0)
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StorageUtils.mergeFiles(config.getPersistencePath(), fileslist, outputFileName, true);
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AnalysisLogger.getLogger().debug("FAOMSY - Deleting parts");
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for (String file:fileslist){
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new File(config.getPersistencePath(),file).delete();
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}
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AnalysisLogger.getLogger().debug("FAOMSY - File assembling complete");
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}
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@Override
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public void postProcess(boolean manageDuplicates, boolean manageFault) {
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try {
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String mainOutputfilename = config.getParam(processOutput);
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String optionalOutputfilename = config.getParam(nonProcessedOutput);
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assembleFiles(mainOutputfilename);
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assembleFiles(optionalOutputfilename);
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AnalysisLogger.getLogger().debug("FAOMSY - Postprocess complete");
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} catch (Exception e) {
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e.printStackTrace();
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}
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}
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}
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@ -0,0 +1,72 @@
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package org.gcube.dataanalysis.executor.tests;
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import java.util.List;
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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.ecoengine.datatypes.StatisticalType;
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import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
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import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory;
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import org.gcube.dataanalysis.ecoengine.test.regression.Regressor;
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import org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing;
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public class RegressionTestFAOMSY {
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/**
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* example of parallel processing on a single machine the procedure will generate a new table for a distribution on suitable species
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*
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*/
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public static AlgorithmConfiguration getConfig() {
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AlgorithmConfiguration config = new AlgorithmConfiguration();
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config.setConfigPath("./cfg/");
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config.setPersistencePath("./");
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config.setParam("DatabaseUserName","utente");
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config.setParam("DatabasePassword","d4science");
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config.setParam("DatabaseURL","jdbc:postgresql://dbtest.research-infrastructures.eu/testdb");
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config.setParam("DatabaseDriver","org.postgresql.Driver");
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AnalysisLogger.setLogger(config.getConfigPath()+AlgorithmConfiguration.defaultLoggerFile);
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return config;
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}
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public static void main(String[] args) throws Exception {
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System.out.println("TEST 1");
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List<ComputationalAgent> generators = GeneratorsFactory.getGenerators(testCMSY());
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generators.get(0).init();
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CustomRegressor.process(generators.get(0));
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StatisticalType output = generators.get(0).getOutput();
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AnalysisLogger.getLogger().debug("Output description: "+output.getDescription());
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generators = null;
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}
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private static AlgorithmConfiguration testCMSY() {
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AlgorithmConfiguration config = getConfig();
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config.setNumberOfResources(5);
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config.setModel("FAOMSY");
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config.setParam("UserName", "gianpaolo.coro");
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// config.setGcubeScope("/gcube");
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config.setGcubeScope("/d4science.research-infrastructures.eu");
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config.setParam("ServiceUserName", "gianpaolo.coro");
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D4ScienceDistributedProcessing.maxMessagesAllowedPerJob=2;
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// config.setParam("StocksFile","http://goo.gl/g6YtVx");
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//config.setParam("StocksFile","https://dl.dropboxusercontent.com/u/12809149/FAOMSY_Short1.csv");
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// config.setParam("StocksFile","https://dl.dropboxusercontent.com/u/12809149/FAOMSY_Short2.csv");
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// config.setParam("StocksFile","https://dl.dropboxusercontent.com/u/12809149/FAOMSY_Longtest.csv");
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config.setParam("StocksFile","http://goo.gl/B09ZL0"); //50species
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//config.setParam("IDsFile","http://goo.gl/9rg3qK");
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// config.setParam("StocksFile","http://goo.gl/Mp2ZLY");
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// config.setParam("StocksFile","http://goo.gl/btuIIe");
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// config.setParam("SelectedStock","Pan_bor_1");
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// config.setParam("SelectedStock","HLH_M08");
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return config;
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}
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}
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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.FileNotFoundException;
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import java.io.FileOutputStream;
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import java.io.FileReader;
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import java.io.FileWriter;
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import java.io.IOException;
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import java.io.InputStream;
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import java.net.URL;
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import java.net.URLConnection;
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import java.util.List;
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import org.gcube.common.scope.api.ScopeProvider;
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import org.gcube.contentmanagement.blobstorage.service.IClient;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.contentmanager.storageclient.model.protocol.smp.Handler;
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import org.gcube.contentmanager.storageclient.wrapper.AccessType;
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import org.gcube.contentmanager.storageclient.wrapper.MemoryType;
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import org.gcube.contentmanager.storageclient.wrapper.StorageClient;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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public class StorageUtils {
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public static void downloadInputFile(String fileurl, String destinationFile) throws Exception{
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try {
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Handler.activateProtocol();
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URL smpFile = new URL(fileurl);
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URLConnection uc = (URLConnection) smpFile.openConnection();
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InputStream is = uc.getInputStream();
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AnalysisLogger.getLogger().debug("GenericWorker-> Retrieving from " + fileurl + " to :" + destinationFile);
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inputStreamToFile(is, destinationFile);
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is.close();
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} catch (Exception e) {
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throw e;
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}
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}
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public static void inputStreamToFile(InputStream is, String path) throws FileNotFoundException, IOException {
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FileOutputStream out = new FileOutputStream(new File(path));
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byte buf[] = new byte[1024];
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int len = 0;
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while ((len = is.read(buf)) > 0)
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out.write(buf, 0, len);
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out.close();
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}
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public static String uploadFilesOnStorage(String scope, String user, String localFolder, String file) throws Exception {
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try {
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ScopeProvider.instance.set(scope);
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AnalysisLogger.getLogger().info("Loading file on scope: " + scope);
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IClient client = new StorageClient(AlgorithmConfiguration.StatisticalManagerClass, AlgorithmConfiguration.StatisticalManagerService, user, AccessType.SHARED, MemoryType.VOLATILE).getClient();
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String remotef = "/"+file;
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||||||
|
client.put(true).LFile(new File(localFolder,file).getAbsolutePath()).RFile(remotef);
|
||||||
|
String url = client.getUrl().RFile(remotef);
|
||||||
|
AnalysisLogger.getLogger().info("Loading finished");
|
||||||
|
System.gc();
|
||||||
|
return url;
|
||||||
|
} catch (Exception e) {
|
||||||
|
AnalysisLogger.getLogger().info("Error in uploading file: " + e.getLocalizedMessage());
|
||||||
|
throw e;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public static int calcFileRows(File file, boolean hasheader){
|
||||||
|
try{
|
||||||
|
BufferedReader br = new BufferedReader(new FileReader(file));
|
||||||
|
String line = br.readLine();
|
||||||
|
if (hasheader)
|
||||||
|
line = br.readLine(); // skip header
|
||||||
|
int counter = 0;
|
||||||
|
while (line!=null){
|
||||||
|
counter++;
|
||||||
|
line = br.readLine();
|
||||||
|
}
|
||||||
|
br.close();
|
||||||
|
return counter;
|
||||||
|
}catch(Exception e){
|
||||||
|
e.printStackTrace();
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
public static void FileSubset(File infile, File outfile, int index, int numberofelements, boolean hasheader) throws Exception{
|
||||||
|
|
||||||
|
BufferedReader br = new BufferedReader(new FileReader(infile));
|
||||||
|
BufferedWriter bw = new BufferedWriter(new FileWriter(outfile));
|
||||||
|
|
||||||
|
String header = null;
|
||||||
|
if (hasheader){
|
||||||
|
header = br.readLine(); // skip header
|
||||||
|
bw.write(header+"\n");
|
||||||
|
}
|
||||||
|
String line = br.readLine();
|
||||||
|
int counter = 0;
|
||||||
|
while (line!=null && counter < (index+numberofelements)){
|
||||||
|
|
||||||
|
if (counter>=index)
|
||||||
|
bw.write(line+"\n");
|
||||||
|
|
||||||
|
counter++;
|
||||||
|
line = br.readLine();
|
||||||
|
}
|
||||||
|
|
||||||
|
br.close();
|
||||||
|
bw.close();
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
public static void downloadFilefromStorage(String scope, String user, String localFolder, String file) throws Exception {
|
||||||
|
try {
|
||||||
|
ScopeProvider.instance.set(scope);
|
||||||
|
AnalysisLogger.getLogger().info("Retrieving file on scope: " + scope);
|
||||||
|
IClient client = new StorageClient(AlgorithmConfiguration.StatisticalManagerClass, AlgorithmConfiguration.StatisticalManagerService, user, AccessType.SHARED, MemoryType.VOLATILE).getClient();
|
||||||
|
String remotef = "/"+file;
|
||||||
|
client.get().LFile(new File(localFolder,file).getAbsolutePath()).RFile(remotef);
|
||||||
|
AnalysisLogger.getLogger().info("Retrieving finished");
|
||||||
|
System.gc();
|
||||||
|
} catch (Exception e) {
|
||||||
|
AnalysisLogger.getLogger().info("Error in retrieving file: " + e.getLocalizedMessage());
|
||||||
|
throw e;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public static void mergeFiles(String localFolder, List<String> filenames, String outputfile, boolean hasheader) throws Exception {
|
||||||
|
try {
|
||||||
|
|
||||||
|
int nfiles = filenames.size();
|
||||||
|
BufferedWriter bw = new BufferedWriter(new FileWriter(outputfile));
|
||||||
|
for (int i=0;i<nfiles;i++){
|
||||||
|
BufferedReader br = new BufferedReader(new FileReader(filenames.get(i)));
|
||||||
|
String header = null;
|
||||||
|
if (hasheader && i==0){
|
||||||
|
header = br.readLine();
|
||||||
|
bw.write(header+"\n");
|
||||||
|
}
|
||||||
|
else if (hasheader)
|
||||||
|
br.readLine();
|
||||||
|
|
||||||
|
String line = br.readLine();
|
||||||
|
while (line!=null){
|
||||||
|
bw.write(line+"\n");
|
||||||
|
line = br.readLine();
|
||||||
|
}
|
||||||
|
|
||||||
|
br.close();
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
bw.close();
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
} catch (Exception e) {
|
||||||
|
AnalysisLogger.getLogger().info("Error in merging files: " + e.getLocalizedMessage());
|
||||||
|
throw e;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
public static void main(String args[]) throws Exception{
|
||||||
|
|
||||||
|
// uploadFilesOnStorage("/gcube", "CMSY", "./", "tacsat.csv");
|
||||||
|
// downloadFilefromStorage("/gcube", "CMSY", "./PARALLEL_PROCESSING", "tacsat.csv");
|
||||||
|
FileSubset(new File("D20_1.csv"), new File("D20_11.csv"), 3, 10, true);
|
||||||
|
}
|
||||||
|
}
|
||||||
Loading…
Reference in New Issue