import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Scanner;
import java.io.*;

import org.apache.commons.lang.StringUtils;

/**
 * @author walshs
 */

class TsvMangler
{

    // The names of these files correspond to functions available in the openBIS
    // interface which are used to add Samples with properties and to attach
    // samples to experiment
    private final String sampleRegisterFile = "SAMPLES_register_from_a_file_and_attach.txt";

    private final String sampleListFile = "SAMPLES_specify_the_list_of_existing_samples.txt";

    // The Data Store Server default incoming directory is needed to
    // write a portion of it's service.properties
    // Assumes login is openBis
    private final String incomingDir = new String("~/sprint/datastore_server/data/incoming");

    // An integer specification the row which contains column headings
    private int headRow;

    // The column headings specified by headRow are stored in header
    private ArrayList<String> header;

    // Rows to ignore
    private ArrayList<Integer> ignoreRow;

    // The columns which define a unique Sample key
    private ArrayList<Integer> keyCols = new ArrayList<Integer>();

    // List of Samples with Properties
    private ArrayList<SampleWithProperties> swp = new ArrayList<SampleWithProperties>();

    // The file to parse
    private String inFile;

    // The name of the DataSet used by the Date Set Server
    private String dataSetName;

    // The name of the experiment
    private String expt;

    // The project name
    private String project;

    // The TSV is stored as an ArrayList of ArrayLists (of Strings)
    private ArrayList<ArrayList<String>> data = new ArrayList<ArrayList<String>>();

    // directory for writing output files
    private String topLevel = new String();

    // Data Set Property Types column config
    private HashMap<Integer, String> dspts = new HashMap<Integer, String>();

    // Sample Property Types column config
    private HashMap<Integer, String> spts = new HashMap<Integer, String>();

    // CONSTRUCTER
    public TsvMangler(int h, ArrayList<Integer> i, String in, ArrayList<Integer> k, String e,
            HashMap<Integer, String> d, String dsn, HashMap<Integer, String> s, String p)
    {
        headRow = h;
        ignoreRow = i;
        inFile = in;
        expt = e;
        dspts = d;
        dataSetName = dsn;
        project = p;

        // Change column specs from 1 based references to 0 based refs
        // for Sample key columns
        Iterator<Integer> iterator = k.iterator();
        while (iterator.hasNext())
        {
            Integer j = new Integer(iterator.next());
            j--;
            keyCols.add(j);

        }

        // Change column specs from 1 based references to 0 based refs
        // for Sample Property Types
        for (Integer foo : s.keySet())
        {
            Integer bar = foo;
            bar--;
            spts.put(bar, s.get(foo));
        }

        loadTsvFile();

        System.out.println("header is size ; " + header.size());
        
        generateSampleKeys();

        topLevel =
                ("/tmp/Tsv2openBIS/" + expt + '/' + System.getProperty("user.name") + "/"
                        + System.currentTimeMillis() + "/");

        File top = new File(topLevel);
        top.mkdirs();

        System.out.println("Writing files to " + topLevel);

    }

    private void loadTsvFile()
    {
        // loads the tsv to memory
        // splits the data and header into seperate structures
        try
        {
            BufferedReader input = new BufferedReader(new FileReader(inFile));
            try
            {
                String line = null;

                Integer lineNum = 0;

                while ((line = input.readLine()) != null)
                {

                  
                    
                    lineNum++;
                    if (line.matches("^\\s+$"))
                    {
                        System.err.println("Skipping line " + lineNum + " as it contains no data");
                        // Weird bug with TSV generated by excel
                        // This line.match skips some empty lines because the println runs
                        // However, it doesn't match all empty lines as some get put into the "data"
                        // ArrayList
                        // Can see this when using the debugger
                        // It's difficult to inspect because the Mac command line tools such as tail
                        // and less
                        // don't recognise /r as a newline break. They display as ^M.
                        // However, the java readLine doesn't have a problem.
                        // Easy quick work around was to go into Excel and delete the blank row of
                        // cells
                        // so that they are truly empty

                    } else
                    {

                        ArrayList<String> dataLine = new ArrayList<String>();

                        Scanner tokenize = new Scanner(line).useDelimiter("\t");
                        while (tokenize.hasNext())
                        {
                            dataLine.add(tokenize.next());
                        }
                        if (lineNum == headRow)
                        {
                            header = dataLine;

                        } else if (ignoreRow.contains(lineNum))
                        {
                            // do nothing
                        } else
                        {
                            data.add(dataLine);
                        }
                    }

                }
            } finally
            {
                input.close();
            }
        } catch (IOException ex)
        {
            ex.printStackTrace();
        }
    }

    private void generateSampleKeys()
    {

        // Generate openBIS SAMPLE IDs
        Iterator<ArrayList<String>> di = data.iterator();
        String key2;

        while (di.hasNext())
        {
            ArrayList<String> row = di.next();

            Iterator<Integer> kci = keyCols.iterator();
            StringBuffer buf = new StringBuffer();
            while (kci.hasNext())
            {
                Integer i = kci.next();
                String value = row.get(i);
                buf.append(value + '_');
            }
            key2 = new String(StringUtils.chop(buf.toString()));
            key2 = key2.toUpperCase();

            SampleWithProperties s = new SampleWithProperties(key2);

            // now have to add properties
            Iterator<Integer> pi = spts.keySet().iterator();
            while (pi.hasNext())
            {
                Integer key3 = pi.next();
                String val = row.get(key3);
                val = val.toUpperCase();
                s.addProperty(spts.get(key3), val);
            }
            swp.add(s);
        }
    }

    
    private String getDataSetPropertiesAsText(){
        
            return StringUtils.join(dspts.values().toArray(),"\n");
    }
    
    
    public void writeDataSetPropertyLoader()
    {

        File f = new File(topLevel + "DataSetProperties.txt");

        String txt =
                "This file simply lists DataSet properties to be registerd for the DataSet "
                        + dataSetName
                        + "\n"
                        + "When the HTTPInvoker API is available this method could write a script to automate\n"
                        + "the registration process\n" + "Anyhow, for now we just list : \n\n"
                        + getDataSetPropertiesAsText();

        try
        {
            BufferedWriter fOut = new BufferedWriter(new FileWriter(f));
            fOut.write(txt);
            fOut.close();
        } catch (Exception e)
        {
            System.err.println("Error: " + e.getMessage());
        }

    }

    public void writeSamplePropertyLoader()
    {

        File f = new File(topLevel + "SampleProperties.txt");

        String txt =
                "This file simply lists Sample properties to be registerd for the sample.\n"
                        + "When the HTTPInvoker API is available this method could write a script to automate\n"
                        + "the registration process\n" + "Anyhow, for now we just list : \n\n"
                        + getSamplePropertiesAsText();

        try
        {
            BufferedWriter fOut = new BufferedWriter(new FileWriter(f));
            fOut.write(txt);
            fOut.close();
        } catch (Exception e)
        {
            System.err.println("Error: " + e.getMessage());
        }

    }

    private Object[] getSamplePropertiesAsArray()
    {

        // Uses the first Samples With Properties object
        // All these object have the same Property Types
        return (swp.get(0)).getPropertyTypes().toArray();

    }

    private String getSamplePropertiesAsText()
    {

        return StringUtils.join(getSamplePropertiesAsArray(), "\n");
    }

    public void writeSamplesFile()
    {

        Iterator<SampleWithProperties> swpi = swp.iterator();
        String head =
                ("identifier\t" + StringUtils.join(getSamplePropertiesAsArray(), "\t") + "\n");
        StringBuffer body = new StringBuffer("");
        StringBuffer sl = new StringBuffer("");

        while (swpi.hasNext())
        {
            SampleWithProperties sample = swpi.next();

            body.append("CISD:/" + project + "/" + sample.getName() + "\t"
                    + StringUtils.join(sample.getPropertyValues().toArray(), "\t") + "\n");
            sl.append(sample.getName() + "\n");
        }

        File f = new File(topLevel + sampleRegisterFile);
        File f2 = new File(topLevel + sampleListFile);

        try
        {
            BufferedWriter fOut = new BufferedWriter(new FileWriter(f));
            fOut.write(head.toString());
            fOut.write(body.toString());
            fOut.close();

            BufferedWriter fOut2 = new BufferedWriter(new FileWriter(f2));
            fOut2.write(sl.toString());
            fOut2.close();

        } catch (Exception e)
        {
            System.err.println("Error: " + e.getMessage());
        }

    }

    private String getConfigFromTemplate(String t)
    {

        StringBuffer sb = new StringBuffer();
        sb.append("\n");
        sb
                .append("# ---------------------------------------------------------------------------\n");
        sb.append("# " + t + " thread configuration\n");
        sb
                .append("# ---------------------------------------------------------------------------\n");
        sb.append("# The directory to watch for incoming data.\n");
        sb.append(t + ".incoming-dir = data/incoming/" + t + "\n");
        sb.append(t + ".incoming-data-completeness-condition = auto-detection\n");
        sb.append(t + ".group-code = " + project + "\n");
        sb.append("# ---------------- Plugin properties\n");
        sb
                .append(t
                        + ".data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor\n");
        sb.append("# following should be set to $ further up the file \n");
        sb
                .append(t
                        + ".data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator}\n");
        sb.append(t + ".data-set-info-extractor.group-code = " + project + "\n");
        sb
                .append(t
                        + ".data-set-info-extractor.data-set-properties-file-name = data-set-properties.tsv\n");
        sb.append(t + ".type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor\n");
        sb.append(t + ".type-extractor.file-format-type = TSV\n");
        sb.append(t + ".type-extractor.locator-type = RELATIVE_LOCATION\n");
        sb.append(t + ".type-extractor.data-set-type = " + t + "\n");
        sb.append(t + ".storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor\n");
        return sb.toString();
    }

    public void writeDssMkdir()
    {

        StringBuffer mkdir = new StringBuffer("#!/bin/bash\n" + "mkdir -v ");
        mkdir.append(incomingDir + "/" + dataSetName + "\n");
        File f = new File(topLevel + "make_incoming_dirs.sh");
        try
        {
            BufferedWriter fOut = new BufferedWriter(new FileWriter(f));
            fOut.write(mkdir.toString());
            fOut.close();
        } catch (Exception e)
        {
            System.err.println("Error: " + e.getMessage());
        }

    }

    public void writeServiceDotProperties()
    {

        String inputsLine = new String("inputs=" + dataSetName);
        StringBuffer config = new StringBuffer();
        String t = getConfigFromTemplate(dataSetName);
        config.append(t);

        String sptext = new String(inputsLine + "\n\n" + config.toString() + "\n\n");

        File f = new File(topLevel + "thread_config_service_properties.txt");
        try
        {
            BufferedWriter fOut = new BufferedWriter(new FileWriter(f));
            fOut.write(sptext);
            fOut.close();

        } catch (Exception e)
        {
            System.err.println("Error: " + e.getMessage());
        }
    }

    public void writeDataForDssUploadOneDirPerRowStyle()
    {

        Iterator<ArrayList<String>> di = data.iterator();
        Iterator<SampleWithProperties> swpi = swp.iterator();
        // each row of data
        while (di.hasNext())
        {
            ArrayList<String> row = di.next();
            String sample = swpi.next().getName();
            // a cell of data
            Iterator<String> ci = row.iterator();
            Iterator<String> hi = header.iterator();

            File path = new File(topLevel + "/DataSet/" + dataSetName + "/" + sample + "/");
            File ftsv = new File(path + "/data-set-properties.tsv");
            File fres = new File(path + "/result.txt");
            try
            {
                path.mkdirs();
                BufferedWriter ftsvOut = new BufferedWriter(new FileWriter(ftsv)); // TSV
                BufferedWriter fresOut = new BufferedWriter(new FileWriter(fres)); // RESULT

                // write the first line of the result file
                while (hi.hasNext())
                {
                    String head = hi.next().toUpperCase();
                    fresOut.write("'" + head + "'" + "\t");
                }
                fresOut.write("\n");

                // write the first line of the data-set-properties file
                ftsvOut.write("property\tvalue\n");

                // write the data and meta-data
                Integer j = 0;
                while (ci.hasNext())
                {
                    j++;
                    //String cell = ci.next().toUpperCase();
                    String cell = ci.next();
                    if (dspts.containsKey(j))
                    {
                        if (cell.equals("")){
                            System.err.println(dspts.get(j) + " is `" + cell + "` for sample " + sample);
                        } else {
                            ftsvOut.write(dspts.get(j) + "\t" + cell + "\n");
                        }
                    }
                    fresOut.write("'" + cell + "'" + "\t");

                }
                
                System.out.println("printed " + j + " cells for sample " + sample + "\n");
                Integer blankCells = header.size() - j;
                System.out.println("need to print " + blankCells + " blank cells\n");
                
                while (blankCells > 0){
                    fresOut.write("''" + "\t");
                    blankCells--;
                }
                
                fresOut.write("\n");

                ftsvOut.close();
                fresOut.close();

            } catch (Exception e)
            {
                System.err.println("Error: " + e.getMessage());
            }
        }
    }
}