datadb/compbio/cassandra/JpredParserLocalFile.java

   1 package compbio.cassandra;
   2
   3 import java.io.BufferedReader;
   4 import java.io.File;
   5 import java.io.FileNotFoundException;
   6 import java.io.IOException;
   7 import java.io.InputStreamReader;
   8 import java.net.HttpURLConnection;
   9 import java.net.MalformedURLException;
  10 import java.io.FileInputStream;
  11 import java.text.ParseException;
  12 import java.text.SimpleDateFormat;
  13 import java.util.ArrayList;
  14 import java.util.Calendar;
  15 import java.util.Date;
  16 import java.util.List;
  17
  18 public class JpredParserLocalFile implements JpredParser {
  19         private CassandraNativeConnector cc = new CassandraNativeConnector();
  20         private String dirprefix;
  21
  22         public void setSource(String newsourceprefix) {
  23                 this.dirprefix = newsourceprefix;
  24         }
  25
  26         JpredParserLocalFile() {
  27                 this.dirprefix = "/home/asherstnev/Projects/Java.projects/proteocache/data_stress_test/data.dat";
  28         }
  29
  30         JpredParserLocalFile(String sourceurl) {
  31                 this.dirprefix = sourceurl;
  32         }
  33
  34         public void Parsing(String source, int nDays) throws IOException {
  35                 Calendar cal = Calendar.getInstance();
  36                 cal.add(Calendar.DATE, -nDays);
  37                 List<String> alljobs = new ArrayList<String>();
  38                 File file = new File(source);
  39                 BufferedReader alljobsfile = new BufferedReader(new InputStreamReader(new FileInputStream(file)));
  40                 String line;
  41
  42                 while ((line = alljobsfile.readLine()) != null) {
  43                         alljobs.add(line);
  44                 }
  45                 alljobsfile.close();
  46
  47                 System.out.println("Inserting jobs for " + nDays + " days, " + alljobs.size() + " jobs in total");
  48                 final long startTime = System.currentTimeMillis();
  49                 for (int i = 0; i < nDays; ++i) {
  50                         cal.add(Calendar.DATE, 1);
  51                         int month = cal.get(Calendar.MONTH) + 1;
  52                         int year = cal.get(Calendar.YEAR);
  53                         int day = cal.get(Calendar.DATE);
  54                         String date = year + "/" + month + "/" + day;
  55                         ParsingForDate(alljobs, date);
  56                 }
  57                 final long execTime = System.currentTimeMillis() - startTime;
  58                 System.out.println("Execution Time = " + execTime + " ms");
  59         }
  60
  61         private int ParsingForDate(List<String> input, String date) {
  62                 int totalcount = 0;
  63                 int countNoData = 0;
  64                 int countUnclearFASTAid = 0;
  65                 int countinsertions = 0;
  66                 int countinserted = 0;
  67                 int counAlignments = 0;
  68                 int countStrange = 0;
  69                 int njobs = 0;
  70
  71                 System.out.println("Inserting jobs for " + date);
  72                 for (String in : input) {
  73                         if (in.matches(date + "(.*)jp_[^\\s]+")) {
  74                                 String[] table = in.split("\\s+");
  75                                 String starttime = table[0];
  76                                 String finishtime = table[1];
  77                                 String ip = table[2];
  78                                 String id = table[table.length - 1];
  79                                 totalcount++;
  80                                 String confilename = dirprefix + "/" + id + "/" + id + ".concise";
  81                                 File confile = new File(confilename);
  82                                 if (confile.exists()) {
  83                                         try {
  84                                                 final FastaReader fr = new FastaReader(confilename);
  85                                                 final List<FastaSequence> seqs = new ArrayList<FastaSequence>();
  86                                                 String newprotein = "";
  87                                                 while (fr.hasNext()) {
  88                                                         final FastaSequence fs = fr.next();
  89                                                         if (fs.getId().equals("QUERY") || fs.getId().equals(id))
  90                                                                 newprotein = fs.getSequence().replaceAll("\n", "");
  91                                                         else if (fs.getId().equals("jnetpred") || fs.getId().equals("JNETPRED")) {
  92                                                                 seqs.add(fs);
  93                                                         }
  94                                                 }
  95                                                 if (newprotein.equals("")) {
  96                                                         countUnclearFASTAid++;
  97                                                 } else {
  98                                                         SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
  99                                                         String dateInString1 = starttime.substring(0, starttime.indexOf(":"));
 100                                                         long insertdate = 0;
 101                                                         try {
 102                                                                 Date dat = formatter.parse(dateInString1);
 103                                                                 insertdate = dat.getTime();
 104                                                         } catch (ParseException e) {
 105                                                                 e.printStackTrace();
 106                                                         }
 107                                                         cc.FormQueryTables(insertdate, starttime, finishtime, ip, id, "OK", "OK", newprotein, seqs);
 108                                                         ++countinsertions;
 109                                                         ++njobs;
 110                                                 }
 111                                                 fr.close();
 112                                         } catch (IOException e) {
 113                                                 e.printStackTrace();
 114                                         }
 115                                 } else {
 116                                         countNoData++;
 117                                 }
 118                         } else {
 119                                 if (in.matches(date + "(.*)Sequence0/(.*)")) {
 120                                         ++counAlignments;
 121                                 } else {
 122                                         ++countStrange;
 123                                 }
 124                         }
 125                 }
 126                 if (true) {
 127                         System.out.println("Total number of jobs = " + totalcount);
 128                         System.out.println("   " + countinserted + " jobs inserted already");
 129                         System.out.println("   " + counAlignments + " jalview jobs");
 130                         System.out.println("   " + countStrange + " not analysed jobs");
 131                         System.out.println("   " + countNoData + " jobs without *.concise.fasta file");
 132                         System.out.println("   " + countUnclearFASTAid + " jobs with unclear FASTA protein id in *.concise.fasta");
 133                         System.out.println("   " + countinsertions + " new job insertions\n");
 134                 }
 135                 return njobs;
 136         }
 137
 138 }