Merge pull request #2414 from jjgao/release-1.6.0

Release 1.6.0

business/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <artifactId>master</artifactId>
     <groupId>org.mskcc.cbio</groupId>
-    <version>1.5.2</version>
+    <version>1.6.0</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>business</artifactId>

core/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <artifactId>master</artifactId>
     <groupId>org.mskcc.cbio</groupId>
-    <version>1.5.2</version>
+    <version>1.6.0</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>core</artifactId>

core/src/main/java/org/mskcc/cbio/portal/dao/DaoCancerStudy.java

@@ -519,6 +519,7 @@ public static void deleteCancerStudy(int internalCancerStudyId) throws DaoExcept
                 "DELETE FROM sample_profile WHERE GENETIC_PROFILE_ID IN (SELECT GENETIC_PROFILE_ID FROM genetic_profile WHERE CANCER_STUDY_ID=?)",
                 "DELETE FROM mutation WHERE GENETIC_PROFILE_ID IN (SELECT GENETIC_PROFILE_ID FROM genetic_profile WHERE CANCER_STUDY_ID=?)",
                 "DELETE FROM mutation_count WHERE GENETIC_PROFILE_ID IN (SELECT GENETIC_PROFILE_ID FROM genetic_profile WHERE CANCER_STUDY_ID=?)",
+                "DELETE FROM mutation_count_by_keyword WHERE GENETIC_PROFILE_ID IN (SELECT GENETIC_PROFILE_ID FROM genetic_profile WHERE CANCER_STUDY_ID=?)",
                 "DELETE FROM clinical_attribute_meta WHERE CANCER_STUDY_ID=?",
                 "DELETE FROM clinical_event_data WHERE CLINICAL_EVENT_ID IN (SELECT CLINICAL_EVENT_ID FROM clinical_event WHERE PATIENT_ID IN (SELECT INTERNAL_ID FROM patient WHERE CANCER_STUDY_ID=?))",
                 "DELETE FROM clinical_event WHERE PATIENT_ID IN (SELECT INTERNAL_ID FROM patient WHERE CANCER_STUDY_ID=?)",

core/src/main/java/org/mskcc/cbio/portal/dao/DaoMutation.java

@@ -145,6 +145,34 @@ public static int calculateMutationCount (int profileId) throws DaoException {
             JdbcUtil.closeAll(DaoMutation.class, con, pstmt, rs);
         }
     }
+
+    public static int calculateMutationCountByKeyword(int profileId) throws DaoException {
+        Connection con = null;
+        PreparedStatement pstmt = null;
+        ResultSet rs = null;
+        try {
+            con = JdbcUtil.getDbConnection(DaoMutation.class);
+            pstmt = con.prepareStatement(
+                "INSERT INTO mutation_count_by_keyword " +
+                    "SELECT g2.`GENETIC_PROFILE_ID`, mutation_event.`KEYWORD`, m2.`ENTREZ_GENE_ID`, " +
+                    "IF(mutation_event.`KEYWORD` IS NULL, 0, COUNT(*)) AS KEYWORD_COUNT, (SELECT COUNT(*) " +
+                    "FROM `mutation` AS m1 , `genetic_profile` AS g1 " +
+                    "WHERE m1.`GENETIC_PROFILE_ID` = g1.`GENETIC_PROFILE_ID` " +
+                    "AND g1.`GENETIC_PROFILE_ID`= g2.`GENETIC_PROFILE_ID` AND m1.`ENTREZ_GENE_ID` = m2.`ENTREZ_GENE_ID` " +
+                    "GROUP BY g1.`GENETIC_PROFILE_ID` , m1.`ENTREZ_GENE_ID`) AS GENE_COUNT " +
+                    "FROM `mutation` AS m2 , `genetic_profile` AS g2 , `mutation_event` " +
+                    "WHERE m2.`GENETIC_PROFILE_ID` = g2.`GENETIC_PROFILE_ID` " +
+                    "AND m2.`MUTATION_EVENT_ID` = mutation_event.`MUTATION_EVENT_ID` " +
+                    "AND g2.`GENETIC_PROFILE_ID`=? " +
+                    "GROUP BY g2.`GENETIC_PROFILE_ID` , mutation_event.`KEYWORD` , m2.`ENTREZ_GENE_ID`;");
+            pstmt.setInt(1, profileId);
+            return pstmt.executeUpdate();
+        } catch (SQLException e) {
+            throw new DaoException(e);
+        } finally {
+            JdbcUtil.closeAll(DaoMutation.class, con, pstmt, rs);
+        }
+    }
 
     /**
      * @deprecated  We believe that this method is no longer called by any part of the codebase, and it will soon be deleted.

core/src/main/java/org/mskcc/cbio/portal/dao/JdbcUtil.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center.
+ * Copyright (c) 2015 - 2017 Memorial Sloan-Kettering Cancer Center.
  *
  * This library is distributed in the hope that it will be useful, but WITHOUT
  * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS
@@ -32,14 +32,12 @@
 
 package org.mskcc.cbio.portal.dao;
 
-import org.mskcc.cbio.portal.util.*;
-
-import org.apache.commons.logging.*;
-
 import java.sql.*;
 import java.util.*;
 import javax.sql.DataSource;
 import org.apache.commons.dbcp.BasicDataSource;
+import org.apache.commons.logging.*;
+import org.mskcc.cbio.portal.util.*;
 
 /**
  * Connection Utility for JDBC.
@@ -48,90 +46,83 @@
  * @author Ersin Ciftci
  */
 public class JdbcUtil {
-    private static DataSource ds;
+    private static DataSource dataSource;
     private static Map<String,Integer> activeConnectionCount = new HashMap<String,Integer>(); // keep track of the number of active connection per class/requester
     private static final Log LOG = LogFactory.getLog(JdbcUtil.class);
-    
+
     /**
      * Gets the data source
      * @return the data source
      */
     public static DataSource getDataSource() {
-        if (ds==null) ds = initDataSource();
-    	return ds;
+        if (dataSource == null) {
+            dataSource = initDataSource();
+        }
+        return dataSource;
     }
-    
+
     /**
      * Sets the data source
      * @param value the data source
      */
     public static void setDataSource(DataSource value) {
-    	ds = value;
+        dataSource = value;
     }
-    
+
     private static DataSource initDataSource() {
         DatabaseProperties dbProperties = DatabaseProperties.getInstance();
         String host = dbProperties.getDbHost();
         String userName = dbProperties.getDbUser();
         String password = dbProperties.getDbPassword();
         String database = dbProperties.getDbName();
-
         String url ="jdbc:mysql://" + host + "/" + database +
                         "?user=" + userName + "&password=" + password +
                         "&zeroDateTimeBehavior=convertToNull";
-
         //  Set up poolable data source
-        BasicDataSource ds = new BasicDataSource();
-        ds.setDriverClassName("com.mysql.jdbc.Driver");
-        ds.setUsername(userName);
-        ds.setPassword(password);
-        ds.setUrl(url);
-
+        BasicDataSource dataSource = new BasicDataSource();
+        dataSource.setDriverClassName("com.mysql.jdbc.Driver");
+        dataSource.setUsername(userName);
+        dataSource.setPassword(password);
+        dataSource.setUrl(url);
         //  By pooling/reusing PreparedStatements, we get a major performance gain
-        ds.setPoolPreparedStatements(true);
-        ds.setMaxActive(100);
-
+        dataSource.setPoolPreparedStatements(true);
+        dataSource.setMaxActive(100);
         activeConnectionCount = new HashMap<String,Integer>();
-
-        return ds;
+        return dataSource;
     }
 
     /**
      * Gets Connection to the Database.
-     * 
+     *
      * @param clazz class
      * @return Live Connection to Database.
      * @throws java.sql.SQLException Error Connecting to Database.
      */
     public static Connection getDbConnection(Class clazz) throws SQLException {
         return getDbConnection(clazz.getName());
     }
-    
+
     /**
      * Gets Connection to the Database.
-     * 
+     *
      * @param requester name
      * @return Live Connection to Database.
      * @throws java.sql.SQLException Error Connecting to Database.
      */
     private static Connection getDbConnection(String requester) throws SQLException {
         // this method should be syncronized
         // but may slow the speed?
-
         Connection con;
         try {
             con = getDataSource().getConnection();
-        }
-        catch (Exception e) {
+        } catch (Exception e) {
             logMessage(e.getMessage());
             throw new SQLException(e);
         }
-
-        if (requester!=null) {
+        if (requester != null) {
             Integer count = activeConnectionCount.get(requester);
-            activeConnectionCount.put(requester, count==null ? 1 : (count+1));
+            activeConnectionCount.put(requester, count == null ? 1 : (count + 1));
         }
-
         return con;
     }
 
@@ -143,19 +134,17 @@ private static Connection getDbConnection(String requester) throws SQLException
     public static void closeConnection(Class clazz, Connection con) {
         closeConnection(clazz.getName(), con);
     }
-    
+
     private static void closeConnection(String requester, Connection con) {
         try {
             if (con != null && !con.isClosed()) {
                 con.close();
-
                 if (requester!=null) {
-                    int count = activeConnectionCount.get(requester)-1;
-                    if (count<0) {
+                    int count = activeConnectionCount.get(requester) - 1;
+                    if (count < 0) {
                         // since adding connection is not synchronized, the count may not be the real one
                         count = 0;
                     }
-
                     activeConnectionCount.put(requester, count);
                 }
             }
@@ -171,8 +160,8 @@ private static void closeConnection(String requester, Connection con) {
      * @param rs  ResultSet Object.
      */
     public static void closeAll(ResultSet rs) {
-                JdbcUtil.closeAll((String)null, null, null, rs);
-        }
+        JdbcUtil.closeAll((String)null, null, null, rs);
+    }
 
     /**
      * Frees Database Connection.
@@ -181,8 +170,7 @@ public static void closeAll(ResultSet rs) {
      * @param ps  Prepared Statement Object.
      * @param rs  ResultSet Object.
      */
-    public static void closeAll(Class clazz, Connection con, PreparedStatement ps,
-            ResultSet rs) {
+    public static void closeAll(Class clazz, Connection con, PreparedStatement ps, ResultSet rs) {
         closeAll(clazz.getName(), con, ps, rs);
     }
 
@@ -192,23 +180,26 @@ public static void closeAll(Class clazz, Connection con, PreparedStatement ps,
      * @param con Connection Object.
      * @param rs  ResultSet Object.
      */
-    private static void closeAll(String requester, Connection con, PreparedStatement ps,
-                                 ResultSet rs) {
+    private static void closeAll(String requester, Connection con, PreparedStatement ps, ResultSet rs) {
         if (rs != null) {
             try {
-                rs.close();
+                if (!rs.isClosed()) {
+                    rs.close();
+                }
             } catch (SQLException e) {
                 e.printStackTrace();
             }
         }
         if (ps != null) {
             try {
-                ps.close();
+                if (!ps.isClosed()) {
+                    ps.close();
+                }
             } catch (SQLException e) {
                 e.printStackTrace();
             }
         }
-        closeConnection(requester, con);        
+        closeConnection(requester, con);
     }
 
     /**
@@ -223,7 +214,9 @@ public static void closeAll(Class clazz, Connection con, ResultSet rs) {
         closeConnection(requester, con);
         if (rs != null) {
             try {
-                rs.close();
+                if (!rs.isClosed()) {
+                    rs.close();
+                }
             } catch (SQLException e) {
                 e.printStackTrace();
             }
@@ -236,18 +229,18 @@ private static void logMessage(String message) {
         }
         System.err.println(message);
     }
-    
+
     // is it good to put the two methods below here?
     static Integer readIntegerFromResultSet(ResultSet rs, String column) throws SQLException {
         int i = rs.getInt(column);
         return rs.wasNull() ? null : i;
     }
-    
+
     static Long readLongFromResultSet(ResultSet rs, String column) throws SQLException {
         long l = rs.getInt(column);
         return rs.wasNull() ? null : l;
     }
-    
+
     static Double readDoubleFromResultSet(ResultSet rs, String column) throws SQLException {
         double d = rs.getDouble(column);
         return rs.wasNull() ? null : d;
@@ -261,7 +254,6 @@ static Double readDoubleFromResultSet(ResultSet rs, String column) throws SQLExc
      * @throws SQLException
      */
     public static void disableForeignKeyCheck(Connection con) throws SQLException {
-
         Statement stmt = con.createStatement();
         stmt.execute("SET FOREIGN_KEY_CHECKS=0");
         stmt.close();
@@ -273,7 +265,6 @@ public static void disableForeignKeyCheck(Connection con) throws SQLException {
      * @throws SQLException
      */
     public static void enableForeignKeyCheck(Connection con) throws SQLException {
-
         Statement stmt = con.createStatement();
         stmt.execute("SET FOREIGN_KEY_CHECKS=1");
         stmt.close();

core/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java

@@ -453,6 +453,7 @@ public void importData() throws IOException, DaoException {
 
                 // calculate mutation count for every sample
                 DaoMutation.calculateMutationCount(geneticProfileId);
+                DaoMutation.calculateMutationCountByKeyword(geneticProfileId);
 
                 if (entriesSkipped > 0) {
                 	ProgressMonitor.setCurrentMessage(" --> total number of data entries skipped (see table below):  " + entriesSkipped);