package compbio.cassandra;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStreamReader;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.io.FileInputStream;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Date;
import java.util.List;

public class JpredParserLocalFile implements JpredParser {
	private CassandraWriter cw = new CassandraWriter();
	private String dirprefix;

	public void setSource(String newsourceprefix) {
		this.dirprefix = newsourceprefix;
	}

	public JpredParserLocalFile() {
		this.dirprefix = "/home/asherstnev/Projects/Java.projects/proteocache/data_stress_test/data.dat";
	}

	public JpredParserLocalFile(String sourceurl) {
		this.dirprefix = sourceurl;
	}

	public void Parsing(String source, int nDays) throws IOException {
		Calendar cal = Calendar.getInstance();
		cal.add(Calendar.DATE, -nDays);
		List<String> alljobs = new ArrayList<String>();
		File file = new File(source);
		BufferedReader alljobsfile = new BufferedReader(new InputStreamReader(new FileInputStream(file)));
		String line;

		while ((line = alljobsfile.readLine()) != null) {
			alljobs.add(line);
		}
		alljobsfile.close();

		System.out.println("Inserting jobs for " + nDays + " days, " + alljobs.size() + " jobs in total");
		final long startTime = System.currentTimeMillis();
		for (int i = 0; i < nDays; ++i) {
			cal.add(Calendar.DATE, 1);
			int month = cal.get(Calendar.MONTH) + 1;
			int year = cal.get(Calendar.YEAR);
			int day = cal.get(Calendar.DATE);
			String date = year + "/" + month + "/" + day;
			ParsingForDate(alljobs, date);
		}
		final long execTime = System.currentTimeMillis() - startTime;
		System.out.println("Execution Time = " + execTime + " ms");
	}

	private void ParsingForDate(List<String> input, String date) {
		int totalcount = 0;
		int countNoData = 0;
		int countUnclearFASTAid = 0;
		int countinsertions = 0;
		int countinserted = 0;
		int counAlignments = 0;
		int countStrange = 0;

		System.out.println("Inserting jobs for " + date);
		for (String in : input) {
			if (in.matches(date + ":(.*)jp_[^\\s]+")) {
				String[] table = in.split("\\s+");
				String starttime = table[0];
				String finishtime = table[1];
				String ip = table[2];
				String id = table[table.length - 1];
				totalcount++;
				String confilename = dirprefix + "/" + id + "/" + id + ".concise";
				File confile = new File(confilename);
				if (confile.exists()) {
					try {
						final FastaReader fr = new FastaReader(confilename);
						final List<FastaSequence> seqs = new ArrayList<FastaSequence>();
						String newprotein = "";
						while (fr.hasNext()) {
							final FastaSequence fs = fr.next();
							if (fs.getId().equals("QUERY") || fs.getId().equals(id))
								newprotein = fs.getSequence().replaceAll("\n", "");
							else if (fs.getId().equals("jnetpred") || fs.getId().equals("JNETPRED")) {
								seqs.add(fs);
							}
						}
						if (newprotein.equals("")) {
							countUnclearFASTAid++;
						} else {
							SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
							String dateInString1 = starttime.substring(0, starttime.indexOf(":"));
							long insertdate = 0;
							try {
								Date dat = formatter.parse(dateInString1);
								insertdate = dat.getTime();
							} catch (ParseException e) {
								e.printStackTrace();
							}
							countinsertions += cw.FormQueryTables(insertdate, starttime, finishtime, ip, id, "OK", "OK", newprotein, seqs);
						}
						fr.close();
					} catch (IOException e) {
						e.printStackTrace();
					}
				} else {
					countNoData++;
				}
			} else {
				if (in.matches(date + "(.*)Sequence0/(.*)")) {
					++counAlignments;
				} else {
					++countStrange;
				}
			}
		}
		if (true) {
			System.out.println("Total number of jobs = " + totalcount);
			System.out.println("   " + countinserted + " jobs inserted already");
			System.out.println("   " + counAlignments + " jalview jobs");
			System.out.println("   " + countStrange + " not analysed jobs");
			System.out.println("   " + countNoData + " jobs without *.concise.fasta file");
			System.out.println("   " + countUnclearFASTAid + " jobs with unclear FASTA protein id in *.concise.fasta");
			System.out.println("   " + countinsertions + " new job insertions\n");
		}
	}

}