package compbio.cassandra;

import java.io.BufferedReader;
import java.io.File;
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 CassandraCreate cc = new CassandraCreate();
	private String dirprefix;

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

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

	public void Parsing(String source, int nDays) {
		Calendar cal = Calendar.getInstance();
		cal.add(Calendar.DATE, -nDays);
		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;
			if (0 < ParsingForDate(source, date)) {
				cc.flushData();
			}
		}
	}

	private int ParsingForDate(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;
		int njobs = 0;

		System.out.println("Inserting jobs for " + date);
		try {
			File file = new File(input);
			BufferedReader alljobs = new BufferedReader(new InputStreamReader(new FileInputStream(file)));
			String line;

			while ((line = alljobs.readLine()) != null) {
				if (line.matches(date + "(.*)jp_[^\\s]+")) {
					String[] table = line.split("\\s+");
					String id = table[table.length - 1];
					totalcount++;
					if (!cc.CheckID(id)) {
						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
										seqs.add(fs);
								}
								if (newprotein.equals("")) {
									countUnclearFASTAid++;
								} else {
									SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
									String dateInString1 = table[0].substring(0, table[0].indexOf(":"));
									long dateWork1 = 0;
									try {
										Date dat1 = formatter.parse(dateInString1);
										dateWork1 = dat1.getTime();
									} catch (ParseException e) {
										e.printStackTrace();
									}
									cc.InsertData(dateWork1, table[0], table[1], table[2], id, "OK", "OK", newprotein, seqs);
									++countinsertions;
									++njobs;
									// flush every 50 insertions
									if (0 == countinsertions % 50) {
										cc.flushData();
										njobs -= 50;
									}
								}
								fr.close();
							} catch (IOException e) {
								e.printStackTrace();
							}
						} else {
							countNoData++;
						}
					} else {
						++countinserted;
					}
				} else {
					if (line.matches(date + "(.*)Sequence0/(.*)")) {
						++counAlignments;
					} else {
						++countStrange;
					}
				}
			}
			alljobs.close();
			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");
		} catch (MalformedURLException e) {
			e.printStackTrace();
		} catch (IOException e) {
			e.printStackTrace();
		}
		return njobs;
	}
}