server/compbio/controllers/ProteomeController.java

   1 package compbio.controllers;
   2
   3 import java.util.Map;
   4
   5 import org.springframework.stereotype.Controller;
   6 import org.springframework.web.bind.annotation.RequestMapping;
   7 import org.springframework.web.bind.annotation.RequestMethod;
   8 import org.springframework.web.bind.annotation.RequestParam;
   9
  10 import compbio.cassandra.readers.FeaturesReader;
  11
  12
  13 /**
  14  * Spring controller for dealing with proteomes. This version works in the
  15  * servlet style.
  16  *
  17  * @author Alexander Sherstnev
  18  * @author Natasha Sherstneva
  19  *
  20  * @since 0.5
  21  * @version 1.0 December 2014
  22  */
  23 @Controller
  24 @RequestMapping("/proteomes")
  25 public class ProteomeController extends BasicController {
  26
  27         @RequestMapping(value = "/load", method = RequestMethod.GET)
  28         public String loadProteome(Map<String, Object> model) {
  29                 model.put("username", getPrincipalName());
  30                 return "support/Notimplemented";
  31         }
  32
  33         @RequestMapping(value = "view", method = RequestMethod.GET)
  34         public String viewProteome(Map<String, Object> model) {
  35                 model.put("username", getPrincipalName());
  36                 return "support/Notimplemented";
  37         }
  38
  39         @RequestMapping(value = "launch", method = RequestMethod.GET)
  40         public String launchjobProteome(Map<String, Object> model) {
  41                 model.put("username", getPrincipalName());
  42                 return "support/Notimplemented";
  43         }
  44
  45         @RequestMapping(value = "load/result", method = RequestMethod.GET)
  46         public String countSequences(@RequestParam("TypeFeatures") String typeFeature, @RequestParam("Percent") String percent,
  47                         Map<String, Object> model) {
  48                 model.put("username", getPrincipalName());
  49                 final long startTime = System.currentTimeMillis();
  50
  51                 if (percent.equals("")) {
  52                         model.put("error", "The value must not be empty");
  53                         model.put("type", typeFeature);
  54                         model.put("value", percent);
  55                         return "query/SSFeatures";
  56                 }
  57
  58                 int realpercent;
  59                 try {
  60                         realpercent = Integer.parseInt(percent.trim());
  61                 } catch (NumberFormatException e) {
  62                         model.put("error", "The value must be an integer number");
  63                         model.put("value", percent);
  64                         return "query/SSFeatures";
  65                 }
  66
  67                 if (realpercent < 1) {
  68                         model.put("error", "The value must be greater than 0");
  69                         model.put("value", percent);
  70                         return "query/SSFeatures";
  71                 }
  72
  73                 if (realpercent > 100) {
  74                         model.put("error", "The value must be less than 100");
  75                         model.put("value", percent);
  76                         return "query/SSFeatures";
  77                 }
  78
  79                 FeaturesReader reader = new FeaturesReader();
  80                 Map<String, String> r = reader.readProteinsPrediction(typeFeature, realpercent);
  81                 model.put("results", r);
  82                 model.put("njobs", 0);
  83                 if (null != r) {
  84                         model.put("njobs", r.size());
  85                 }
  86                 final long endTime = System.currentTimeMillis();
  87                 model.put("timeExecution", (endTime - startTime));
  88                 model.put("feature", typeFeature);
  89                 model.put("percent", realpercent);
  90                 return "reports/SSFeatures";
  91         }
  92
  93 }