X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=server%2Fcompbio%2Fcontrollers%2FSequenceController.java;h=df4c98720e03b1936a2a2653aa919a50ccb354e1;hb=025c55d49c191f24d0e06c5cbb69a9894c50af22;hp=d4afbdc635bafff0a95f52e3a1059dd272fca9e7;hpb=ca0ed055669c0c5d81689e52da5325578a221888;p=proteocache.git

diff --git a/server/compbio/controllers/SequenceController.java b/server/compbio/controllers/SequenceController.java
index d4afbdc..df4c987 100644
--- a/server/compbio/controllers/SequenceController.java
+++ b/server/compbio/controllers/SequenceController.java
@@ -2,51 +2,82 @@ 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.DataBase;
-
+import compbio.cassandra.ProteinBean;
+import compbio.cassandra.TotalByCounterBean;
 import compbio.statistic.CassandraRequester;
 
 /**
+ * Spring controller for sequence queries. 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 {
+@RequestMapping("/sequence")
+public class SequenceController extends BasicController {
+
+	/**
+	 * 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
 		String trimmedsequence = sequence.replaceAll("\\s", "");
+		if (trimmedsequence.equalsIgnoreCase("")) {
+			model.put("error", "The sequence cann't be empty");
+			model.put("value", sequence);
+			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 "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<DataBase> r = cr.readProteins(trimmedsequence, flag);
+			List<ProteinBean> r = cr.readProteins(trimmedsequence, searchtype);
 			model.put("results", r);
 			if (null != r) {
-				System.out.println("result size = " + r.size());
-				model.put("njobs", r.size());
+				if (searchtype.equals("whole"))
+					model.put("njobs", r.get(0).getJobid().size());
+				else
+					model.put("njobs", r.size());
 			}
 		}
 		final long endTime = System.currentTimeMillis();
@@ -54,18 +85,34 @@ public class SequenceController {
 		return "reportProteinSequences";
 	}
 
-	@RequestMapping(value = "/sequence/querycounter", method = RequestMethod.GET)
-	public String countSequences(@RequestParam("counterJob") int counter, Map<String, Object> model) {
+	@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 < 1) {
+		if (counter.equals("")) {
+			model.put("error", "The value must not be empty");
+			model.put("value", counter);
+			return "query/SequenceCounts";
+		}
+
+		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 "query/SequenceCounts";
+		}
+
+		if (realcounter < 1) {
 			model.put("error", "The value must be greater than 0");
 			model.put("value", counter);
-			return "queryProteinSequenceCounter";
+			return "query/SequenceCounts";
 		}
 
 		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 +120,7 @@ public class SequenceController {
 		}
 		final long endTime = System.currentTimeMillis();
 		model.put("timeExecution", (endTime - startTime));
-		model.put("counter", counter);
+		model.put("counter", realcounter);
 		return "reportProteinSequencesCounter";
 	}