Merge branch 'DAO'

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

diff --git a/server/compbio/controllers/SequenceController.java b/server/compbio/controllers/SequenceController.java
index 105ef2f..76b5e20 100644 (file)
--- a/server/compbio/controllers/SequenceController.java
+++ b/server/compbio/controllers/SequenceController.java
@@ -1,5 +1,6 @@
 package compbio.controllers;
 
+import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.regex.Pattern;
@@ -13,11 +14,10 @@ import compbio.beans.ProteinBean;
 import compbio.beans.TotalByCounterBean;
 import compbio.cassandra.readers.ReaderByCounter;
 import compbio.cassandra.readers.SequenceReader;
-import compbio.statistic.CassandraRequester;
 
 /**
- * Spring controller for sequence queries. This version works in the servlet
- * style.
+ * Spring controller for supporting sequence queries. This version works in the
+ * servlet style.
  * 
  * @author Alexander Sherstnev
  * @author Natasha Sherstneva
@@ -36,7 +36,7 @@ public class SequenceController extends BasicController {
 
        /**
         * form a query page for search protein sequence. The servlet should be
-        * available for users and admins only. 
+        * available for users and admins only.
         * 
         * @param model
         *            MVC model
@@ -50,8 +50,8 @@ public class SequenceController extends BasicController {
        }
 
        /**
-        * form a query page for statistics: Protein by job count. The servlet should be
-        * available for users and admins only. 
+        * form a query page for statistics: Protein by job count. The servlet
+        * should be available for users and admins only.
         * 
         * @param model
         *            MVC model
@@ -72,10 +72,11 @@ public class SequenceController extends BasicController {
         * @param sequence
         *            protein sequence or part of sequence
         * @param searchtype
-        *            defined whether the whole sequence or part of sequence would be searched
+        *            defined whether the whole sequence or part of sequence would
+        *            be searched
         * @return link to the report JSP page
         */
-       @RequestMapping(value = "sequence/results", method = RequestMethod.GET)
+       @RequestMapping(value = "results", method = RequestMethod.GET)
        public String findSequence(@RequestParam("sequence") String sequence, @RequestParam("searchtype") String searchtype,
                        Map<String, Object> model) {
                model.put("username", getPrincipalName());
@@ -97,21 +98,41 @@ public class SequenceController extends BasicController {
                model.put("njobs", 0);
                model.put("prot", trimmedsequence);
                model.put("searchtype", searchtype);
-
+               StringBuilder csvline = new StringBuilder("");
                if (0 < trimmedsequence.length()) {
                        SequenceReader reader = new SequenceReader();
                        List<ProteinBean> result = reader.readProteins(trimmedsequence, searchtype);
                        model.put("results", result);
                        if (null != result) {
-                               if (searchtype.equals("whole"))
+                               if (searchtype.equals("whole")) {
                                        model.put("njobs", result.get(0).getJobid().size());
-                               else
+                               } else {
                                        model.put("njobs", result.size());
+                               }
+                               csvline.append("\'Job\',\'Annotation\',\'Sequence\'%0A");
+                               for (ProteinBean entry : result) {
+                                       List<String> jobs = entry.getJobid();
+                                       String protein = entry.getSequence();
+                                       LinkedHashMap<String, String> predictions = entry.getPredictions();
+                                       StringBuilder jobline = new StringBuilder();
+                                       for (Map.Entry<String, String> pr : predictions.entrySet()) {
+                                               jobline.append("\'\',\'" + pr.getKey() + "\',\'" + pr.getValue() + "\'%0A");
+                                       }
+                                       for (String job : jobs) {
+                                               csvline.append("\'" + job + "\',\'Sequence\',\'" + protein + "\',\'%0A" + jobline.toString());
+                                       }
+                               }
                        }
+               } else {
+                       model.put("error", "The sequence after trimming is empty");
+                       model.put("value", sequence);
+                       return "query/Sequence";
                }
+               model.put("csvfile", csvline.toString());
+
                final long endTime = System.currentTimeMillis();
                model.put("timeExecution", (endTime - startTime));
-               return "reportProteinSequences";
+               return "reports/Sequences";
        }
 
        /**
@@ -120,7 +141,7 @@ public class SequenceController extends BasicController {
         * @param model
         *            MVC model object
         * @param counter
-        *           
+        * 
         * @return link to the report JSP page
         */
        @RequestMapping(value = "counts/results", method = RequestMethod.GET)
@@ -150,17 +171,32 @@ public class SequenceController extends BasicController {
                }
 
                ReaderByCounter reader = new ReaderByCounter();
-
                List<TotalByCounterBean> r = reader.readProteinByCounter(realcounter);
                model.put("results", r);
                model.put("njobs", 0);
+               StringBuilder csvline = new StringBuilder("");
                if (null != r) {
                        model.put("njobs", r.size());
+                       // form line for CSV file
+                       csvline.append("\'Job%20 count\', \'Protein%20Sequence\'%0A");
+                       for (TotalByCounterBean b : r) {
+                               if (b.getName().equals("")) {
+                                       // fix problem with records without protein sequence
+                                       // (alignment jobs)
+                                       csvline.append("\'" + b.getTotaljobs() + "\',\'Alignment%20job\'%0A");
+                                       b.setName("Alignment job");
+                               } else {
+                                       csvline.append("\'" + b.getTotaljobs() + "\',\'" + b.getName() + "\'%0A");
+                               }
+                       }
                }
+               model.put("csvfile", csvline.toString());
+
+               model.put("results", r);
                final long endTime = System.currentTimeMillis();
                model.put("timeExecution", (endTime - startTime));
                model.put("counter", realcounter);
-               return "reportProteinSequencesCounter";
+               return "reports/SequencesStatistics";
        }
 
 }