Merge branch 'servlets' of https://source.jalview.org/git/proteocache into servlets

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

diff --git a/server/compbio/controllers/SequenceController.java b/server/compbio/controllers/SequenceController.java
index d4afbdc..62ec81e 100644 (file)
--- a/server/compbio/controllers/SequenceController.java
+++ b/server/compbio/controllers/SequenceController.java
@@ -2,22 +2,35 @@ package compbio.controllers;
 
 import java.util.List;
 import java.util.Map;
+import java.util.regex.Pattern;
 
 import org.springframework.stereotype.Controller;
 import org.springframework.web.bind.annotation.RequestMapping;
 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.
+ * 
  * @author Alexander Sherstnev
  * @author Natasha Sherstneva
+ * 
+ * @since 0.5
+ * @version 1.0 December 2013
  */
 @Controller
 public class SequenceController {
+       
+       /**
+        * 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) {
@@ -35,18 +48,32 @@ public class SequenceController {
        public String findSequence(@RequestParam("sequence") String sequence, @RequestParam("protein") String flag, Map<String, Object> model) {
                final long startTime = System.currentTimeMillis();
 
+               // input checks
                String trimmedsequence = sequence.replaceAll("\\s", "");
+               if (trimmedsequence.equalsIgnoreCase("")) {
+                       model.put("error", "The sequence cann't be empty");
+                       model.put("value", sequence);
+                       return "queryProteinSequence";
+               }
+               if (NONPROTEIN.matcher(trimmedsequence).find()) {
+                       model.put("error", "The sequence contains symbols not from the standard protein alphabet");
+                       model.put("value", sequence);
+                       return "queryProteinSequence";
+               }
+
                model.put("njobs", 0);
                model.put("prot", trimmedsequence);
                model.put("flag", flag);
 
                if (0 < trimmedsequence.length()) {
                        CassandraRequester cr = new CassandraRequester();
-                       List<DataBase> r = cr.readProteins(trimmedsequence, flag);
+                       List<ProteinBean> r = cr.readProteins(trimmedsequence, flag);
                        model.put("results", r);
                        if (null != r) {
-                               System.out.println("result size = " + r.size());
-                               model.put("njobs", r.size());
+                               if (flag.equals("whole"))
+                                       model.put("njobs",r.get(0).getJobid().size());
+                               else
+                                       model.put("njobs", r.size());
                        }
                }
                final long endTime = System.currentTimeMillis();
@@ -55,17 +82,32 @@ public class SequenceController {
        }
 
        @RequestMapping(value = "/sequence/querycounter", method = RequestMethod.GET)
-       public String countSequences(@RequestParam("counterJob") int counter, Map<String, Object> model) {
+       public String countSequences(@RequestParam("counterJob") String counter, Map<String, Object> model) {
                final long startTime = System.currentTimeMillis();
 
-               if (counter < 1) {
+               if (counter.equals("")) {
+                       model.put("error", "The value must not be empty");
+                       model.put("value", counter);
+                       return "queryIPStatistics";
+               }
+
+               int realcounter;
+               try {
+                       realcounter = Integer.parseInt(counter.trim());
+               } catch (NumberFormatException e) {
+                       model.put("error", "The value must be an integer number");
+                       model.put("value", counter);
+                       return "queryIPStatistics";
+               }
+
+               if (realcounter < 1) {
                        model.put("error", "The value must be greater than 0");
                        model.put("value", counter);
-                       return "queryProteinSequenceCounter";
+                       return "queryIPStatistics";
                }
 
                CassandraRequester cr = new CassandraRequester();
-               List<DataBase> r = cr.readProteinByCounter(counter);
+               List<TotalByCounterBean> r = cr.readProteinByCounter(realcounter);
                model.put("results", r);
                model.put("njobs", 0);
                if (null != r) {
@@ -73,7 +115,7 @@ public class SequenceController {
                }
                final long endTime = System.currentTimeMillis();
                model.put("timeExecution", (endTime - startTime));
-               model.put("counter", counter);
+               model.put("counter", realcounter);
                return "reportProteinSequencesCounter";
        }