server/compbio/controllers/SequenceController.java

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