datadb/compbio/cassandra/JpredParserHTTP.java

   1 package compbio.cassandra;
   2
   3 import java.io.BufferedReader;
   4 import java.io.FileNotFoundException;
   5 import java.io.IOException;
   6 import java.io.InputStream;
   7 import java.io.InputStreamReader;
   8 import java.net.HttpURLConnection;
   9 import java.net.MalformedURLException;
  10 import java.net.URL;
  11 import java.net.URLConnection;
  12 import java.util.ArrayList;
  13 import java.util.Calendar;
  14 import java.util.Date;
  15 import java.util.List;
  16 import java.util.regex.Matcher;
  17 import java.util.regex.Pattern;
  18
  19 import compbio.cassandra.JpredParser;
  20 import compbio.data.sequence.FastaReader;
  21 import compbio.data.sequence.FastaSequence;
  22 import compbio.engine.JpredJob;
  23 import compbio.engine.ProteoCachePropertyHelperManager;
  24 import compbio.engine.archive.Archive;
  25 import compbio.engine.archive.ArchivedJob;
  26 import compbio.util.PropertyHelper;
  27 import compbio.util.Util;
  28
  29 public class JpredParserHTTP implements JpredParser {
  30         private CassandraWriter cw = new CassandraWriter();
  31         private static Archive archive;
  32         private String dirprefix;
  33         private List<FastaSequence> alignment;
  34         private List<FastaSequence> predictions;
  35         private int countNoData;
  36         private static boolean archiving = false;
  37         private static final PropertyHelper ph = ProteoCachePropertyHelperManager.getPropertyHelper();
  38
  39         public JpredParserHTTP() {
  40                 dirprefix = "http://www.compbio.dundee.ac.uk/www-jpred/results";
  41         }
  42
  43         public JpredParserHTTP(String sourceurl) {
  44                 dirprefix = sourceurl;
  45         }
  46
  47         public void setSource(String newsourceprefix) {
  48                 dirprefix = newsourceprefix;
  49         }
  50
  51         private boolean initBooleanValue(String key) {
  52                 assert key != null;
  53                 String status = ph.getProperty(key);
  54                 if (Util.isEmpty(status)) {
  55                         return false;
  56                 }
  57                 return new Boolean(status.trim()).booleanValue();
  58         }
  59
  60         public void Parsing(String source, int nDays) throws IOException {
  61                 Calendar cal = Calendar.getInstance();
  62                 cal.add(Calendar.DATE, -nDays);
  63                 archiving = initBooleanValue("archive.enable");
  64                 if (archiving) {
  65                         archive = new Archive();
  66                 }
  67                 for (int i = 0; i < nDays; ++i) {
  68                         cal.add(Calendar.DATE, 1);
  69                         String date = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DATE);
  70                         ParsingOneDay(source, date);
  71                 }
  72         }
  73
  74         /*
  75          * The method parses the Jpred output concise file in the FASTA format If
  76          * there is a record with ID = QUERY or jobid, this a "one protein" job
  77          * otherwise this is an alignment job
  78          */
  79         private String parsePredictions(final InputStream stream, String jobid) throws FileNotFoundException {
  80                 final FastaReader fr = new FastaReader(stream);
  81                 String protein = "";
  82                 while (fr.hasNext()) {
  83                         final FastaSequence fs = fr.next();
  84                         String seqid = fs.getId();
  85                         String seq = fs.getSequence().replaceAll("\n", "");
  86                         if (seqid.equals("jnetpred") || seqid.equals("Lupas_21") || seqid.equals("Lupas_14") || seqid.equals("Lupas_28")
  87                                         || seqid.equals("JNETSOL25") || seqid.equals("JNETSOL5") || seqid.equals("JNETSOL0") || seqid.equals("JNETCONF")
  88                                         || seqid.equals("JNETHMM") || seqid.equals("JNETPSSM") || seqid.equals("JNETCONF")) {
  89                                 predictions.add(fs);
  90                         } else {
  91                                 alignment.add(fs);
  92                                 if (seqid.equals("QUERY") || seqid.equals(jobid))
  93                                         protein = seq;
  94                         }
  95                 }
  96                 return protein;
  97         }
  98
  99         private String parseSeqFile(final InputStream stream, String jobid) throws FileNotFoundException {
 100                 final FastaReader fr = new FastaReader(stream);
 101                 String protein = "";
 102                 final FastaSequence fs = fr.next();
 103                 protein = fs.getSequence().replaceAll("\n", "");
 104                 if (fr.hasNext()) {
 105                         // this is an aligment job...
 106                         return "alignment";
 107                 }
 108                 return protein;
 109         }
 110
 111         private String parseLogFile(final InputStream stream, JpredJob job) throws IOException {
 112                 String out = "";
 113                 BufferedReader buffer = new BufferedReader(new InputStreamReader(stream));
 114                 String line;
 115                 if (null != (out = buffer.readLine()) && (out.contains("version"))) {
 116                         Matcher matcher = Pattern.compile("((\\d|\\.)+)").matcher(out);
 117                         if (matcher.find())
 118                                 job.setVersion(matcher.group(0));
 119                 }
 120                 while (null != (line = buffer.readLine())) {
 121                         out += line;
 122                 }
 123                 return out;
 124         }
 125
 126         private int analyseJob(String[] jobinfo) throws IOException {
 127                 alignment = new ArrayList<FastaSequence>();
 128                 predictions = new ArrayList<FastaSequence>();
 129                 boolean running = true;
 130                 boolean ConcisefileExists = false;
 131                 boolean LogfileExists = false;
 132                 JpredJob job = new JpredJob(jobinfo[jobinfo.length - 1], jobinfo[0], jobinfo[1]);
 133                 job.setIP(jobinfo[2]);
 134                 Date currDate = new Date();
 135                 String maindir = dirprefix + "/" + job.getJobID() + "/";
 136
 137                 try {
 138                         URL dirurl = new URL(maindir);
 139                         HttpURLConnection httpConnection_dirurl = (HttpURLConnection) dirurl.openConnection();
 140                         if (httpConnection_dirurl.getResponseCode() < 199 || 300 <= httpConnection_dirurl.getResponseCode()) {
 141                                 return 0;
 142                         }
 143                         URL conciseurl = new URL(maindir + job.getJobID() + ".concise.fasta");
 144                         URL logurl = new URL(maindir + "LOG");
 145                         HttpURLConnection httpConnection_conciseurl = (HttpURLConnection) conciseurl.openConnection();
 146                         HttpURLConnection httpConnection_logurl = (HttpURLConnection) logurl.openConnection();
 147                         if (199 < httpConnection_conciseurl.getResponseCode() && httpConnection_conciseurl.getResponseCode() < 300) {
 148                                 ConcisefileExists = true;
 149                                 running = false;
 150                                 try {
 151                                         job.setProtein(parsePredictions(conciseurl.openStream(), job.getJobID()));
 152                                 } catch (IOException e) {
 153                                         e.printStackTrace();
 154                                 }
 155                         } else {
 156                                 // The job still can be running of failed...
 157                                 ++countNoData;
 158                         }
 159                         if (199 < httpConnection_logurl.getResponseCode() && httpConnection_logurl.getResponseCode() < 300) {
 160                                 LogfileExists = true;
 161                                 job.setProgrammeName("Jpred");
 162                                 job.setLog(parseLogFile(logurl.openStream(), job));
 163                         } else {
 164                                 // The job has not been started at all...
 165                                 job.setExecutionStatus("FAIL");
 166                                 job.setFinalStatus("STOPPED");
 167                                 running = false;
 168                         }
 169                         if (job.getLog().matches("(.*)TIMEOUT\\syour\\sjob\\stimed\\sout(.*)")) {
 170                                 // blast job was too long (more than 3600 secs by default)...
 171                                 job.setExecutionStatus("FAIL");
 172                                 job.setFinalStatus("TIMEDOUT");
 173                                 running = false;
 174                         } else if (job.getLog().matches("(.*)Jpred\\serror:\\sDied\\sat(.*)")) {
 175                                 // an internal Jpred error...
 176                                 job.setExecutionStatus("FAIL");
 177                                 job.setFinalStatus("JPREDERROR");
 178                                 running = false;
 179                         } else if ((currDate.getTime() - job.getEndTime()) / 1000 > 3601 && LogfileExists && !ConcisefileExists) {
 180                                 // the job was stopped with unknown reason...
 181                                 job.setExecutionStatus("FAIL");
 182                                 job.setFinalStatus("STOPPED");
 183                                 running = false;
 184                         }
 185
 186                         httpConnection_conciseurl.disconnect();
 187                         httpConnection_logurl.disconnect();
 188                 } catch (MalformedURLException e) {
 189                         e.printStackTrace();
 190                 }
 191
 192                 if (!running) {
 193                         // logging the job
 194                         job.setAlignment(alignment);
 195                         job.setPredictions(predictions);
 196                         if (job.getExecutionStatus().equals("FAIL")) {
 197                                 URL sequrl = new URL(maindir + job.getJobID() + ".seq");
 198                                 HttpURLConnection httpConnection_sequrl = (HttpURLConnection) sequrl.openConnection();
 199                                 if (199 < httpConnection_sequrl.getResponseCode() && httpConnection_sequrl.getResponseCode() < 300) {
 200                                         try {
 201                                                 job.setProtein(parseSeqFile(sequrl.openStream(), job.getJobID()));
 202                                         } catch (IOException e) {
 203                                                 e.printStackTrace();
 204                                         }
 205                                 }
 206                         }
 207                         cw.FormQueryTables(job);
 208
 209                         // archiving the job
 210                         if (archiving) {
 211                                 ArchivedJob ajob = new ArchivedJob(job.getJobID());
 212                                 String arlink = archive.createJob(job.getJobID());
 213                                 if (job.getFinalStatus().equals("OK")) {
 214                                         ajob.setArchivePath(arlink);
 215                                         ajob.copyArchiveFromWeb(maindir + job.getJobID() + ".tar.gz");
 216                                         cw.ArchiveData(job, arlink);
 217                                 } else {
 218                                         cw.ArchiveData(job, "undefined");
 219                                 }
 220                         }
 221                         return 1;
 222                 }
 223
 224                 return 0;
 225         }
 226
 227         private void ParsingOneDay(String input, String date) {
 228                 int totalcount = 0;
 229                 int countinsertions = 0;
 230                 int countinserted = 0;
 231                 int countNotanalyzed = 0;
 232                 countNoData = 0;
 233
 234                 System.out.println("Inserting jobs for " + date);
 235                 try {
 236                         URL url = new URL(input);
 237                         URLConnection conn = url.openConnection();
 238                         BufferedReader alljobs = new BufferedReader(new InputStreamReader(conn.getInputStream()));
 239                         String line;
 240
 241                         while ((line = alljobs.readLine()) != null) {
 242                                 if (line.matches(date + ":(.*)jp_[^\\s]+")) {
 243                                         totalcount++;
 244                                         String[] job = line.split("\\s+");
 245                                         String jobid = job[job.length - 1];
 246                                         if (cw.JobisNotInsterted(jobid)) {
 247                                                 countinsertions += analyseJob(job);
 248                                         } else {
 249                                                 ++countinserted;
 250                                         }
 251                                 } else {
 252                                         ++countNotanalyzed;
 253                                 }
 254                         }
 255                         alljobs.close();
 256                         System.out.println("Total number of jobs = " + totalcount);
 257                         System.out.println("   " + countinserted + " jobs inserted already");
 258                         System.out.println("   " + countNotanalyzed + " not analysed jobs");
 259                         System.out.println("   " + countNoData + " jobs without *.concise.fasta file (RUNNING or FAILED)");
 260                         System.out.println("   " + countinsertions + " new job insertions\n");
 261                 } catch (MalformedURLException e) {
 262                         e.printStackTrace();
 263                 } catch (IOException e) {
 264                         e.printStackTrace();
 265                 }
 266                 ;
 267         }
 268 };