server/compbio/controllers/SequenceController.java

   1 package compbio.controllers;
   2
   3 import java.security.Principal;
   4 import java.util.List;
   5 import java.util.Map;
   6 import java.util.regex.Pattern;
   7
   8 import org.springframework.stereotype.Controller;
   9 import org.springframework.web.bind.annotation.RequestMapping;
  10 import org.springframework.web.bind.annotation.RequestMethod;
  11 import org.springframework.web.bind.annotation.RequestParam;
  12
  13 import compbio.cassandra.ProteinBean;
  14 import compbio.cassandra.TotalByCounterBean;
  15 import compbio.statistic.CassandraRequester;
  16
  17 /**
  18  * Spring controller for sequence queries. This version works in the servlet
  19  * style.
  20  *
  21  * @author Alexander Sherstnev
  22  * @author Natasha Sherstneva
  23  *
  24  * @since 0.5
  25  * @version 1.0 December 2013
  26  */
  27 @Controller
  28 @RequestMapping("/sequence")
  29 public class SequenceController {
  30
  31         /**
  32          * pattern for NON-protein alphabet symbols
  33          */
  34         private final Pattern NONPROTEIN = Pattern.compile("[^ARNDCQEGHILKMFPSTWYV]+", Pattern.CASE_INSENSITIVE);
  35
  36         @RequestMapping(value = "query", method = RequestMethod.GET)
  37         public String formSequenceQuery(Map<String, Object> model, Principal principal) {
  38                 model.put("username", principal.getName());
  39                 model.put("value", "AAAAA");
  40                 return "queryProteinSequence";
  41         }
  42
  43         @RequestMapping(value = "counts/query", method = RequestMethod.GET)
  44         public String formCounterQuery(Map<String, Object> model, Principal principal) {
  45                 model.put("username", principal.getName());
  46                 model.put("value", 5);
  47                 return "queryProteinSequenceCounter";
  48         }
  49
  50         @RequestMapping(value = "sequence/results", method = RequestMethod.GET)
  51         public String findSequence(@RequestParam("sequence") String sequence, @RequestParam("protein") String flag, Map<String, Object> model,
  52                         Principal principal) {
  53                 model.put("username", principal.getName());
  54                 final long startTime = System.currentTimeMillis();
  55
  56                 // input checks
  57                 String trimmedsequence = sequence.replaceAll("\\s", "");
  58                 if (trimmedsequence.equalsIgnoreCase("")) {
  59                         model.put("error", "The sequence cann't be empty");
  60                         model.put("value", sequence);
  61                         return "queryProteinSequence";
  62                 }
  63                 if (NONPROTEIN.matcher(trimmedsequence).find()) {
  64                         model.put("error", "The sequence contains symbols not from the standard protein alphabet");
  65                         model.put("value", sequence);
  66                         return "queryProteinSequence";
  67                 }
  68
  69                 model.put("njobs", 0);
  70                 model.put("prot", trimmedsequence);
  71                 model.put("flag", flag);
  72
  73                 if (0 < trimmedsequence.length()) {
  74                         CassandraRequester cr = new CassandraRequester();
  75                         List<ProteinBean> r = cr.readProteins(trimmedsequence, flag);
  76                         model.put("results", r);
  77                         if (null != r) {
  78                                 if (flag.equals("whole"))
  79                                         model.put("njobs", r.get(0).getJobid().size());
  80                                 else
  81                                         model.put("njobs", r.size());
  82                         }
  83                 }
  84                 final long endTime = System.currentTimeMillis();
  85                 model.put("timeExecution", (endTime - startTime));
  86                 return "reportProteinSequences";
  87         }
  88
  89         @RequestMapping(value = "counts/results", method = RequestMethod.GET)
  90         public String countSequences(@RequestParam("counterJob") String counter, Map<String, Object> model, Principal principal) {
  91                 model.put("username", principal.getName());
  92                 final long startTime = System.currentTimeMillis();
  93
  94                 if (counter.equals("")) {
  95                         model.put("error", "The value must not be empty");
  96                         model.put("value", counter);
  97                         return "queryIPStatistics";
  98                 }
  99
 100                 int realcounter;
 101                 try {
 102                         realcounter = Integer.parseInt(counter.trim());
 103                 } catch (NumberFormatException e) {
 104                         model.put("error", "The value must be an integer number");
 105                         model.put("value", counter);
 106                         return "queryIPStatistics";
 107                 }
 108
 109                 if (realcounter < 1) {
 110                         model.put("error", "The value must be greater than 0");
 111                         model.put("value", counter);
 112                         return "queryIPStatistics";
 113                 }
 114
 115                 CassandraRequester cr = new CassandraRequester();
 116                 List<TotalByCounterBean> r = cr.readProteinByCounter(realcounter);
 117                 model.put("results", r);
 118                 model.put("njobs", 0);
 119                 if (null != r) {
 120                         model.put("njobs", r.size());
 121                 }
 122                 final long endTime = System.currentTimeMillis();
 123                 model.put("timeExecution", (endTime - startTime));
 124                 model.put("counter", realcounter);
 125                 return "reportProteinSequencesCounter";
 126         }
 127
 128 }