package compbio.cassandra;

import java.io.BufferedReader;
import java.io.DataInputStream;
import java.io.EOFException;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLConnection;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Date;
import java.util.List;

import compbio.cassandra.JpredParser;

public class JpredParserHTTP implements JpredParser {
	private CassandraWriter cw = new CassandraWriter();
	private String dirprefix;
	private List<FastaSequence> alignment;
	private List<FastaSequence> predictions;
	private String jnetpred;

	public JpredParserHTTP() {
		dirprefix = "http://www.compbio.dundee.ac.uk/www-jpred/results";
	}

	public JpredParserHTTP(String sourceurl) {
		dirprefix = sourceurl;
	}

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

	public void Parsing(String source, int nDays) throws IOException {
		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;
			ParsingForDate(source, date);
		}
	}

	private String parsePredictions(final InputStream stream, String jobid) throws FileNotFoundException {
		final FastaReader fr = new FastaReader(stream);
		String query = "";
		alignment = new ArrayList<FastaSequence>();
		predictions = new ArrayList<FastaSequence>();
		while (fr.hasNext()) {
			final FastaSequence fs = fr.next();
			String seqid = fs.getId();
			String seq = fs.getSequence().replaceAll("\n", "");
			if (seqid.equals("QUERY") || seqid.equals(jobid)) {
				query = seq;
				alignment.add(fs);
			} else if (seqid.equals("jnetpred") || seqid.equals("Lupas_21") || seqid.equals("Lupas_14") || seqid.equals("Lupas_28")
					|| seqid.equals("JNETSOL25") || seqid.equals("JNETSOL5") || seqid.equals("JNETSOL0") || seqid.equals("JNETCONF")
					|| seqid.equals("JNETHMM") || seqid.equals("JNETPSSM")) {
				predictions.add(fs);
				if (seqid.equals("jnetpred"))
					jnetpred = seq;
			} else {
				alignment.add(fs);
			}
		}
		return query;
	}

	private String parseLogFile(final InputStream stream) throws IOException {
		String out = "";
		BufferedReader buffer = new BufferedReader(new InputStreamReader(stream));
		String line;
		while (null != (line = buffer.readLine())) {
			out += line;
		}
		return out;
	}

	private List<Byte> parseArchiveFile(final InputStream stream) throws IOException {
		DataInputStream data_in = new DataInputStream(stream);
		List<Byte> out = new ArrayList<Byte>();
		while (true) {
			try {
				out.add(data_in.readByte());
			} catch (EOFException eof) {
				break;
			}
		}
		return out;
	}

	private void 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;

		System.out.println("Inserting jobs for " + date);
		try {
			URL url = new URL(input);
			URLConnection conn = url.openConnection();
			BufferedReader alljobs = new BufferedReader(new InputStreamReader(conn.getInputStream()));
			String line;

			while ((line = alljobs.readLine()) != null) {
				if (line.matches(date + ":(.*)jp_[^\\s]+")) {
					String[] table = line.split("\\s+");
					// Format of a record:
					// starttime endtime ip email jobid (directory)
					// 013/10/25:21:55:7 2013/10/25:21:59:13 201.239.98.172
					// unknown_email jp_J9HBCBT
					String id = table[table.length - 1];
					totalcount++;
					if (cw.JobisNotInsterted(id)) {
						URL dataurl = new URL(dirprefix + "/" + id + "/" + id + ".concise.fasta");
						URL archiveurl = new URL(dirprefix + "/" + id + "/" + id + ".tar.gz");
						URL logurl = new URL(dirprefix + "/" + id + "/LOG");
						HttpURLConnection httpConnection1 = (HttpURLConnection) dataurl.openConnection();
						HttpURLConnection httpConnection2 = (HttpURLConnection) logurl.openConnection();
						HttpURLConnection httpConnection3 = (HttpURLConnection) archiveurl.openConnection();
						int response1 = httpConnection1.getResponseCode();
						int response2 = httpConnection2.getResponseCode();
						if (199 < response1 && response1 < 300) {
							try {
								String protein = parsePredictions(dataurl.openStream(), id);
								if (protein.equals("")) {
									countUnclearFASTAid++;
								} else {
									SimpleDateFormat dateformatter = new SimpleDateFormat("yyyy/MM/dd");
									SimpleDateFormat timeformatter = new SimpleDateFormat("yyyy/MM/dd:H:m:s");
									String startdatestring = table[0].substring(0, table[0].indexOf(":"));
									try {
										Date startdate = dateformatter.parse(startdatestring);
										Date starttime = timeformatter.parse(table[0]);
										Date endtime = timeformatter.parse(table[1]);
										String ip = table[2];
										String execstatus = "OK";
										String finalstatus = "OK";
										countinsertions += cw.FormQueryTables(startdate.getTime(), table[0], table[1], ip, id, execstatus,
												finalstatus, protein, predictions);

										long exectime = (endtime.getTime() - starttime.getTime()) / 1000;
										String log = "";
										if (199 < response2 && response2 < 300) {
											log = parseLogFile(logurl.openStream());
										}
										cw.ArchiveData(startdate.getTime(), exectime, ip, id, execstatus, finalstatus, protein,
												predictions, alignment, log, archiveurl.toString());
									} catch (ParseException e) {
										e.printStackTrace();
									}
								}
							} catch (IOException e) {
								e.printStackTrace();
							}
						} else {
							countNoData++;
						}
						httpConnection1.disconnect();
						httpConnection2.disconnect();
						httpConnection3.disconnect();
					} 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();
		}
		;
	}
}