minor bug fixed, code clean and code refactoring

pom.xml

@@ -20,11 +20,6 @@
             <artifactId>mysql-connector-java</artifactId>
             <version>8.0.17</version>
         </dependency>
-        <dependency>
-            <groupId>org.apache.tomcat</groupId>
-            <artifactId>tomcat-jdbc</artifactId>
-            <version>8.0.30</version>
-        </dependency>
         <dependency>
             <groupId>javax</groupId>
             <artifactId>javaee-web-api</artifactId>

src/main/java/controller/Search.java

@@ -23,9 +23,16 @@
  */
 public class Search extends HttpServlet {
 
+    // it should change to use session instead, but having a issue lost session from alias site
+    private static String dbVersion = "v3";
+
     protected void processRequest(HttpServletRequest request, HttpServletResponse response)
             throws ServletException, IOException {
         try {
+            if (request.getParameter("version") != null) {
+                dbVersion = request.getParameter("version");
+            }
+
             List<VariantGeneScore> variantGeneScoreList = new ArrayList<>();
 
             if (request.getParameter("query") != null) {
@@ -35,13 +42,15 @@ protected void processRequest(HttpServletRequest request, HttpServletResponse re
                 // search by gene or region or variant
                 String query = request.getParameter("query").toUpperCase().replaceAll("( )+", "");
 
-                checkRegionValid(request, query);
+                boolean isRegionValid = checkRegionValid(request, query);
 
-                String dbVersion = initDBVersion(request);
                 Output.init(query, dbVersion, variantGeneScoreList);
 
                 request.setAttribute("query", query);
+                request.setAttribute("version", dbVersion);
+                request.setAttribute("isTruncated", Output.isTruncated(variantGeneScoreList));
                 request.setAttribute("variantGeneScoreList", variantGeneScoreList);
+                request.setAttribute("isRegionValid", isRegionValid);
             }
 
             final String content_type = request.getParameter("content-type");
@@ -56,30 +65,17 @@ protected void processRequest(HttpServletRequest request, HttpServletResponse re
         }
     }
 
-    private String initDBVersion(HttpServletRequest request) {
-        String dbVersion = (String) request.getSession().getAttribute("version");
-
-        if (request.getParameter("version") != null) {
-            dbVersion = request.getParameter("version");
-            request.getSession().setAttribute("version", dbVersion);
-        }
-
-        return dbVersion;
-    }
-
-    private void checkRegionValid(HttpServletRequest request, String query) {
-        boolean isRegionValid = true;
-
+    private boolean checkRegionValid(HttpServletRequest request, String query) {
         if (query.contains(":")) { // search region
             String[] tmp = query.split(":"); // chr:start-end
             tmp = tmp[1].split("-");
             int start = Integer.valueOf(tmp[0]);
             int end = Integer.valueOf(tmp[1]);
 
-            isRegionValid = Output.isRegionValid(start, end);
+            return Output.isRegionValid(start, end);
+        } else {
+            return true;
         }
-
-        request.getSession().setAttribute("isRegionValid", isRegionValid);
     }
 
     @Override

src/main/java/model/Output.java

@@ -14,6 +14,7 @@
  */
 public class Output {
 
+    private static final int maxDisplayNum = 1000;
     private static final int maxRowToQuery = 5000;
     private static final int maxBaseNumToDisplay = 10000;
 
@@ -249,4 +250,14 @@ private static List<String> getEnsgGeneNameByHgnc(String hgnc, String dbVersion)
 
         return ensgList;
     }
+
+    public static boolean isTruncated(List<VariantGeneScore> variantGeneScoreList) {
+        if (variantGeneScoreList.size() <= maxDisplayNum) {
+            return false;
+        } else {
+            // hack to restrict only display 1000 rows
+            variantGeneScoreList = variantGeneScoreList.subList(0, maxDisplayNum);
+            return true;
+        }
+    }
 }

src/main/java/util/DBManager.java

@@ -2,16 +2,15 @@
 
 import java.sql.*;
 import java.util.HashMap;
-import org.apache.tomcat.jdbc.pool.DataSource;
-import org.apache.tomcat.jdbc.pool.PoolProperties;
 
 /**
  *
  * @author nick
  */
 public class DBManager {
 
-    private static DataSource dataSource;
+    private static Connection connection;
+    private static Statement statement;
 
     private static String dbUrl;
     private static String dbUser;
@@ -21,36 +20,15 @@ public class DBManager {
     private static String dbVersionName = "v1:vdsdb,v2:trap_v2_060117,v3:trap_v3";
 
     public static void init() throws Exception {
-        initDBVersion();
+        if (connection == null || connection.isClosed()) {
+            initDBVersion();
 
-        initDataFromSystemConfig();
-
-        if (dataSource == null) {
-            PoolProperties p = new PoolProperties();
-            p.setDriverClassName("com.mysql.cj.jdbc.Driver");
-            p.setUrl(dbUrl);
-            p.setUsername(dbUser);
-            p.setPassword(dbPassword);
-            p.setJmxEnabled(true);
-            p.setTestWhileIdle(false);
-            p.setTestOnBorrow(true);
-            p.setValidationQuery("SELECT 1");
-            p.setTestOnReturn(false);
-            p.setValidationInterval(30000);
-            p.setTimeBetweenEvictionRunsMillis(30000);
-            p.setMaxActive(100);
-            p.setInitialSize(10);
-            p.setMaxWait(10000);
-            p.setRemoveAbandonedTimeout(60);
-            p.setMinEvictableIdleTimeMillis(30000);
-            p.setMinIdle(10);
-            p.setLogAbandoned(true);
-            p.setRemoveAbandoned(true);
-            p.setJdbcInterceptors(
-                    "org.apache.tomcat.jdbc.pool.interceptor.ConnectionState;"
-                    + "org.apache.tomcat.jdbc.pool.interceptor.StatementFinalizer");
-            dataSource = new DataSource();
-            dataSource.setPoolProperties(p);
+            initDataFromSystemConfig();
+            Class.forName("com.mysql.cj.jdbc.Driver");
+            connection = DriverManager.getConnection(dbUrl, dbUser, dbPassword);
+            statement = connection.createStatement();
+        } else if (statement.isClosed()) {
+            statement = connection.createStatement();
         }
     }
 
@@ -81,11 +59,11 @@ private static void initDataFromSystemConfig() {
     }
 
     public static ResultSet executeQuery(String sqlQuery) throws SQLException {
-        return dataSource.getConnection().createStatement().executeQuery(sqlQuery);
+        return statement.executeQuery(sqlQuery);
     }
 
     public static PreparedStatement prepareStatement(String sqlQuery) throws SQLException {
-        return dataSource.getConnection().prepareStatement(sqlQuery);
+        return connection.prepareStatement(sqlQuery);
     }
 
     public static String getDBName(String dbVersion) {

src/main/webapp/index.jsp

@@ -32,11 +32,11 @@
                         </div>
 
                         <%
-                            String version = (String) request.getSession().getAttribute("version");
+                            String version = (String) request.getAttribute("version");
 
                             if (version == null) {
                                 version = "v3";
-                                request.getSession().setAttribute("version", version);
+                                request.setAttribute("version", version);
                             }
                         %>
 

src/main/webapp/result.jsp

@@ -4,7 +4,8 @@
 
 <%
     String query = (String) request.getAttribute("query");
-    Boolean isRegionValid = (Boolean) request.getSession().getAttribute("isRegionValid");
+    Boolean isRegionValid = (Boolean) request.getAttribute("isRegionValid");
+    Boolean isTruncated = (Boolean) request.getAttribute("isTruncated");
     List<VariantGeneScore> variantGeneScoreList
             = (List<VariantGeneScore>) request.getAttribute("variantGeneScoreList");
 
@@ -13,7 +14,7 @@
 <div class="row">
     <div class="col-md-10">
         <h4>
-            Data version: <mark><%=request.getSession().getAttribute("version")%></mark>
+            Data version: <mark><%=request.getAttribute("version")%></mark>
         </h4>
     </div>
 </div>
@@ -46,6 +47,15 @@
 </div>
 <%
 } else {
+    if (isTruncated) {
+%>
+<div class="alert alert-warning" style="width:90%">
+    <h4>
+        Please notice that the displayed variant list is truncated. To obtain the full database please refer to the terms of use.
+    </h4>
+</div>
+<%
+    }
 %>  
 <table class="table table-striped">
     <thead>