1. Move query jsps into a separate directory

[proteocache.git] / server / compbio / controllers / SequenceController.java

diff --git a/server/compbio/controllers/SequenceController.java b/server/compbio/controllers/SequenceController.java
index 62ec81e..df4c987 100644 (file)
--- a/server/compbio/controllers/SequenceController.java
+++ b/server/compbio/controllers/SequenceController.java
@@ -10,13 +10,12 @@ import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.RequestParam;
 
 import compbio.cassandra.ProteinBean;
-import compbio.cassandra.DataBase;
-import compbio.data.sequence.SequenceUtil;
 import compbio.cassandra.TotalByCounterBean;
 import compbio.statistic.CassandraRequester;
 
 /**
- * Spring controller for sequence search. This version works in the servlet style.
+ * Spring controller for sequence queries. This version works in the servlet
+ * style.
  * 
  * @author Alexander Sherstnev
  * @author Natasha Sherstneva
@@ -25,27 +24,32 @@ import compbio.statistic.CassandraRequester;
  * @version 1.0 December 2013
  */
 @Controller
-public class SequenceController {
-       
+@RequestMapping("/sequence")
+public class SequenceController extends BasicController {
+
        /**
-        * pattern for NON-protein alphabet  symbols
+        * pattern for NON-protein alphabet symbols
         */
        private final Pattern NONPROTEIN = Pattern.compile("[^ARNDCQEGHILKMFPSTWYV]+", Pattern.CASE_INSENSITIVE);
 
-       @RequestMapping(value = "/sequence/query1", method = RequestMethod.GET)
+       @RequestMapping(value = "query", method = RequestMethod.GET)
        public String formSequenceQuery(Map<String, Object> model) {
+               model.put("username", getPrincipalName());
                model.put("value", "AAAAA");
-               return "queryProteinSequence";
+               return "query/Sequence";
        }
 
-       @RequestMapping(value = "/sequence/query2", method = RequestMethod.GET)
+       @RequestMapping(value = "counts/query", method = RequestMethod.GET)
        public String formCounterQuery(Map<String, Object> model) {
+               model.put("username", getPrincipalName());
                model.put("value", 5);
-               return "queryProteinSequenceCounter";
+               return "query/SequenceCounts";
        }
-       
-       @RequestMapping(value = "/sequence/querysequence", method = RequestMethod.GET)
-       public String findSequence(@RequestParam("sequence") String sequence, @RequestParam("protein") String flag, Map<String, Object> model) {
+
+       @RequestMapping(value = "sequence/results", method = RequestMethod.GET)
+       public String findSequence(@RequestParam("sequence") String sequence, @RequestParam("searchtype") String searchtype,
+                       Map<String, Object> model) {
+               model.put("username", getPrincipalName());
                final long startTime = System.currentTimeMillis();
 
                // input checks
@@ -53,25 +57,25 @@ public class SequenceController {
                if (trimmedsequence.equalsIgnoreCase("")) {
                        model.put("error", "The sequence cann't be empty");
                        model.put("value", sequence);
-                       return "queryProteinSequence";
+                       return "query/Sequence";
                }
                if (NONPROTEIN.matcher(trimmedsequence).find()) {
                        model.put("error", "The sequence contains symbols not from the standard protein alphabet");
                        model.put("value", sequence);
-                       return "queryProteinSequence";
+                       return "query/Sequence";
                }
 
                model.put("njobs", 0);
                model.put("prot", trimmedsequence);
-               model.put("flag", flag);
+               model.put("searchtype", searchtype);
 
                if (0 < trimmedsequence.length()) {
                        CassandraRequester cr = new CassandraRequester();
-                       List<ProteinBean> r = cr.readProteins(trimmedsequence, flag);
+                       List<ProteinBean> r = cr.readProteins(trimmedsequence, searchtype);
                        model.put("results", r);
                        if (null != r) {
-                               if (flag.equals("whole"))
-                                       model.put("njobs",r.get(0).getJobid().size());
+                               if (searchtype.equals("whole"))
+                                       model.put("njobs", r.get(0).getJobid().size());
                                else
                                        model.put("njobs", r.size());
                        }
@@ -81,14 +85,15 @@ public class SequenceController {
                return "reportProteinSequences";
        }
 
-       @RequestMapping(value = "/sequence/querycounter", method = RequestMethod.GET)
+       @RequestMapping(value = "counts/results", method = RequestMethod.GET)
        public String countSequences(@RequestParam("counterJob") String counter, Map<String, Object> model) {
+               model.put("username", getPrincipalName());
                final long startTime = System.currentTimeMillis();
 
                if (counter.equals("")) {
                        model.put("error", "The value must not be empty");
                        model.put("value", counter);
-                       return "queryIPStatistics";
+                       return "query/SequenceCounts";
                }
 
                int realcounter;
@@ -97,13 +102,13 @@ public class SequenceController {
                } catch (NumberFormatException e) {
                        model.put("error", "The value must be an integer number");
                        model.put("value", counter);
-                       return "queryIPStatistics";
+                       return "query/SequenceCounts";
                }
 
                if (realcounter < 1) {
                        model.put("error", "The value must be greater than 0");
                        model.put("value", counter);
-                       return "queryIPStatistics";
+                       return "query/SequenceCounts";
                }
 
                CassandraRequester cr = new CassandraRequester();