Rename and merge controllers

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

diff --git a/server/compbio/controllers/SequenceController.java b/server/compbio/controllers/SequenceController.java
index 0f154d3..6440d74 100644 (file)
--- a/server/compbio/controllers/SequenceController.java
+++ b/server/compbio/controllers/SequenceController.java
@@ -1,5 +1,6 @@
 package compbio.controllers;
 
+import java.security.Principal;
 import java.util.List;
 import java.util.Map;
 import java.util.regex.Pattern;
@@ -10,12 +11,12 @@ 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
@@ -24,27 +25,32 @@ import compbio.statistic.CassandraRequester;
  * @version 1.0 December 2013
  */
 @Controller
+@RequestMapping("/sequence")
 public class SequenceController {
-       
+
        /**
-        * 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)
-       public String formSequenceQuery(Map<String, Object> model) {
+       @RequestMapping(value = "query", method = RequestMethod.GET)
+       public String formSequenceQuery(Map<String, Object> model, Principal principal) {
+               model.put("username", principal.getName());
                model.put("value", "AAAAA");
                return "queryProteinSequence";
        }
 
-       @RequestMapping(value = "/sequence/query2", method = RequestMethod.GET)
-       public String formCounterQuery(Map<String, Object> model) {
+       @RequestMapping(value = "counts/query", method = RequestMethod.GET)
+       public String formCounterQuery(Map<String, Object> model, Principal principal) {
+               model.put("username", principal.getName());
                model.put("value", 5);
                return "queryProteinSequenceCounter";
        }
-       
-       @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("protein") String flag, Map<String, Object> model,
+                       Principal principal) {
+               model.put("username", principal.getName());
                final long startTime = System.currentTimeMillis();
 
                // input checks
@@ -70,7 +76,7 @@ public class SequenceController {
                        model.put("results", r);
                        if (null != r) {
                                if (flag.equals("whole"))
-                                       model.put("njobs",r.get(0).getJobid().size());
+                                       model.put("njobs", r.get(0).getJobid().size());
                                else
                                        model.put("njobs", r.size());
                        }
@@ -80,8 +86,9 @@ public class SequenceController {
                return "reportProteinSequences";
        }
 
-       @RequestMapping(value = "/sequence/querycounter", method = RequestMethod.GET)
-       public String countSequences(@RequestParam("counterJob") String counter, Map<String, Object> model) {
+       @RequestMapping(value = "counts/results", method = RequestMethod.GET)
+       public String countSequences(@RequestParam("counterJob") String counter, Map<String, Object> model, Principal principal) {
+               model.put("username", principal.getName());
                final long startTime = System.currentTimeMillis();
 
                if (counter.equals("")) {
@@ -106,7 +113,7 @@ public class SequenceController {
                }
 
                CassandraRequester cr = new CassandraRequester();
-               List<DataBase> r = cr.readProteinByCounter(realcounter);
+               List<TotalByCounterBean> r = cr.readProteinByCounter(realcounter);
                model.put("results", r);
                model.put("njobs", 0);
                if (null != r) {