repast.simphony.R.RWizard.java Source code

Introduction

Here is the source code for repast.simphony.R.RWizard.java

Source

package repast.simphony.R;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileWriter;
import java.io.FilenameFilter;
import java.io.IOException;
import java.io.InputStreamReader;
import java.nio.file.FileSystems;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import org.apache.commons.lang3.SystemUtils;

import repast.simphony.data.analysis.AnalysisPluginWizard;
import repast.simphony.data2.DataSetRegistry;
import repast.simphony.data2.FileDataSink;
import repast.simphony.data2.FormatType;
import repast.simphony.data2.Formatter;
import repast.simphony.util.SystemConstants;

/**
 * A wizard for executing R on a file outputter's output.
 * 
 * @author Eric Tatara
 * @author Jerry Vos
 */

public class RWizard extends AnalysisPluginWizard {

    private static final String R_HOME = "./RHome/";

    private Map<String, String> envVars = new HashMap<String, String>();

    public RWizard() {

    }

    public RWizard(DataSetRegistry loggingRegistry, boolean showCopyright, boolean browseForRHome, String name,
            String installHome, String defaultLocation, String licenseFileName) {

        super(loggingRegistry, showCopyright, browseForRHome, name, installHome, defaultLocation, licenseFileName);
    }

    // this must be called after getExecutionCommand
    public Map<String, String> getEnvVars() {
        return envVars;
    }

    public String[] getExecutionCommand() {

        List<String> commands = new ArrayList<String>();

        // NOTE: the LOGFILE and DELIMMTER args are processed by our .Rprofile.

        if (SystemUtils.IS_OS_WINDOWS) {
            //commands.add("R_PROFILE_USER=" + prepFileNameForR(getRHome()));
            //commands.add("&");

            envVars.put("R_PROFILE_USER", prepFileNameForR(getRHome()) + ".Rprofile");
            //commands.add("SET R_PROFILE_USER=" + prepFileNameForR(getRHome()));

            //builder.append("& ");
            List<FileDataSink> outputters = fileStep.getChosenOutputters();

            // For each outputter, define the log file and delimitter
            for (int i = 0; i < outputters.size(); i++) {
                Path out = outputters.get(i).getFile().toPath().normalize().toAbsolutePath();
                Path cwd = FileSystems.getDefault().getPath(".").normalize().toAbsolutePath();
                //System.out.println(out);
                //System.out.println(cwd);
                String sout = out.toString();
                if (out.startsWith(cwd)) {
                    sout = sout.substring(cwd.toString().length() + 1);
                }

                envVars.put("LOG_FILE" + i, sout.replace("\\", "/"));
                Formatter formatter = outputters.get(i).getFormatter();
                if (outputters.get(i).getFormat() != FormatType.TABULAR) {
                    LOG.warn("When invoking R, an outputter without a delimited formatter "
                            + "was found. R can only be invoked on output files with using a delimiter.");
                    break;
                }
                String delimiter = formatter.getDelimiter();
                envVars.put("DELIMITER" + i, delimiter);
            }
            commands.add(getInstallHome());
        } else if (SystemUtils.IS_OS_MAC) {
            List<FileDataSink> outputters = fileStep.getChosenOutputters();
            List<String> files = new ArrayList<String>();
            List<String> delims = new ArrayList<String>();
            String cwd = new File(".").getAbsolutePath();
            for (int i = 0; i < outputters.size(); i++) {
                Formatter formatter = outputters.get(i).getFormatter();
                if (outputters.get(i).getFormat() != FormatType.TABULAR) {
                    LOG.warn("When invoking R, an outputter without a delimited formatter "
                            + "was found. R can only be invoked on output files with using a delimiter.");
                    break;
                }
                delims.add(formatter.getDelimiter());
                String fileName = outputters.get(i).getFile().getAbsolutePath();
                File f = new File(fileName);
                if (fileName.startsWith("/")) {
                    files.add(fileName);
                } else {
                    if (f.exists()) {
                        files.add("./" + fileName);
                    } else {
                        // assume its relative to the current working directory
                        files.add(cwd + "/" + fileName);
                    }
                }
            }

            for (int i = 0; i < files.size(); i++) {
                envVars.put("LOG_FILE" + i, files.get(i));
                envVars.put("DELIMITER" + i, delims.get(i));
            }

            // this should ceate the .RProfile file
            getRHome();
            envVars.put("R_PROFILE_USER", cwd + "/RHome/.RProfile");
            commands.add("open");
            commands.add("-n");
            commands.add(getInstallHome());
            commands.add(cwd);

        } else {
            // TODO linux command
        }

        return commands.toArray(new String[commands.size()]);
    }

    protected String prepFileNameForR(String fileName) {
        return fileName.replace('\\', '/');
    }

    private String getRHome() {
        File rHomeDir = new File(R_HOME);

        // create the RHome directory in the runtime dir if not present
        if (!rHomeDir.exists()) {
            rHomeDir.mkdir();
        }

        // copy .Rprofile to the user's R Home
        // check if it exists already as /RHome/.Rprofile
        if (rHomeDir.list(new FilenameFilter() {
            public boolean accept(File dir, String name) {
                if (name.equals(".Rprofile")) {
                    return true;
                }
                return false;
            }
        }).length == 0) {

            // if /RHome/.Rprofile doesnt exist make a new one from Rprofile.txt
            try {
                BufferedReader reader = new BufferedReader(
                        new InputStreamReader(RWizard.class.getResourceAsStream("Rprofile.txt")));

                FileWriter writer = new FileWriter(R_HOME + ".Rprofile");

                String line = reader.readLine();
                while (line != null) {
                    writer.write(line + SystemConstants.LINE_SEPARATOR);

                    line = reader.readLine();
                }
                reader.close();
                writer.close();
            } catch (IOException e) {
                LOG.error("RWizard.getRHome: Error, preparing the R home "
                        + "directory.  The execution of R may not occur properly.", e);
            }
        }

        return R_HOME;
    }

    @Override
    public String getCannotRunMessage() {
        // TODO Auto-generated method stub
        return null;
    }
}