From 00be8b205de51ea251771b3e7b43a9d0d27f6904 Mon Sep 17 00:00:00 2001
From: Robert Sheridan <7747489+sheridancbio@users.noreply.github.com>
Date: Mon, 18 Mar 2024 16:43:37 -0400
Subject: [PATCH] update mysql-connector-java to 8.0.28

- fix one ResultSet.first() function call which is now illegal for
        a forward only result set (the default type)
---
 pom.xml                                            |  2 +-
 .../org/mskcc/cbio/portal/dao/JdbcDataSource.java  |  5 ++++-
 .../org/mskcc/cbio/portal/dao/MySQLbulkLoader.java |  4 +---
 .../applicationContext-persistenceConnections.xml  | 14 +++++++++++++-
 src/test/resources/applicationContext-dao.xml      | 12 ++++++++++++
 5 files changed, 31 insertions(+), 6 deletions(-)

diff --git a/pom.xml b/pom.xml
index 3b030136..802d5ce8 100644
--- a/pom.xml
+++ b/pom.xml
@@ -24,7 +24,7 @@
 		<maf.version>1.0.0</maf.version>
 
 
-		<mysql_driver.version>5.1.48</mysql_driver.version>
+		<mysql_driver.version>8.0.28</mysql_driver.version>
 		<mysql_commons_lang3.version>3.13.0</mysql_commons_lang3.version>
 
 		<commons_dbcp2.version>2.10.0</commons_dbcp2.version>
diff --git a/src/main/java/org/mskcc/cbio/portal/dao/JdbcDataSource.java b/src/main/java/org/mskcc/cbio/portal/dao/JdbcDataSource.java
index a16ef9f9..eb8a1a32 100644
--- a/src/main/java/org/mskcc/cbio/portal/dao/JdbcDataSource.java
+++ b/src/main/java/org/mskcc/cbio/portal/dao/JdbcDataSource.java
@@ -38,7 +38,7 @@ public String getLabel() {
         }
     }
 
-    public JdbcDataSource () {
+    public JdbcDataSource() {
         DatabaseProperties dbProperties = DatabaseProperties.getInstance();
         logUsedDeprecatedProperties(dbProperties);
         // extract required property values
@@ -65,6 +65,9 @@ public JdbcDataSource () {
         this.setDriverClassName(mysqlDriverClassName);
         // Disable this to avoid caching statements
         this.setPoolPreparedStatements(Boolean.valueOf(enablePooling));
+        // this property setting is needed to enable MySQLbulkLoader to load data from a local file
+        // this is set here in case this class is initialized via JdbcUtil (not expected), but is also set in applicationContext resource files.
+        this.addConnectionProperty("allowLoadLocalInfile", "true");
         // these values are from the production cbioportal application context for a jndi data source
         this.setMaxTotal(500);
         this.setMaxIdle(30);
diff --git a/src/main/java/org/mskcc/cbio/portal/dao/MySQLbulkLoader.java b/src/main/java/org/mskcc/cbio/portal/dao/MySQLbulkLoader.java
index c9b23e64..3414fc4b 100644
--- a/src/main/java/org/mskcc/cbio/portal/dao/MySQLbulkLoader.java
+++ b/src/main/java/org/mskcc/cbio/portal/dao/MySQLbulkLoader.java
@@ -84,10 +84,8 @@ public static int flushAll() throws DaoException {
             con = JdbcUtil.getDbConnection(MySQLbulkLoader.class);
             stmt = con.prepareStatement("SELECT @@foreign_key_checks;");
             ResultSet result = stmt.executeQuery();
-            
-            result.first();
+            result.next();
             checks = result.getInt(1);
-
             stmt = con.prepareStatement("SET foreign_key_checks = ?;");
             stmt.setLong(1, 0);
             stmt.execute();
diff --git a/src/main/resources/applicationContext-persistenceConnections.xml b/src/main/resources/applicationContext-persistenceConnections.xml
index 91b9737a..82ce4aa5 100644
--- a/src/main/resources/applicationContext-persistenceConnections.xml
+++ b/src/main/resources/applicationContext-persistenceConnections.xml
@@ -74,6 +74,17 @@
             <property name="mapperLocations" value="classpath*:org/cbioportal/persistence/mybatis/**/*.xml" />
             <property name="databaseIdProvider" ref="databaseIdProvider"/>
         </bean>
+        <!-- configure the data source to allow LOAD DATA LOCAL INFILE ... -->
+        <bean class="org.springframework.beans.factory.config.MethodInvokingFactoryBean">
+            <property name="targetObject" ref="businessDataSource"/>
+            <property name="targetMethod" value="addConnectionProperty"/>
+            <property name="arguments">
+                <list>
+                    <value>allowLoadLocalInfile</value>
+                    <value>true</value>
+                </list>
+            </property>
+        </bean>
     </beans>
 
     <beans profile="dbcp">
@@ -98,4 +109,5 @@
             </property>
         </bean>
     </beans>
-</beans>
\ No newline at end of file
+
+</beans>
diff --git a/src/test/resources/applicationContext-dao.xml b/src/test/resources/applicationContext-dao.xml
index 5e5fce64..e0fbe55b 100644
--- a/src/test/resources/applicationContext-dao.xml
+++ b/src/test/resources/applicationContext-dao.xml
@@ -88,6 +88,18 @@
         <property name="databaseIdProvider" ref="databaseIdProvider"/>
     </bean>
     
+    <!-- configure the data source to allow LOAD DATA LOCAL INFILE ... -->
+    <b:bean class="org.springframework.beans.factory.config.MethodInvokingFactoryBean">
+        <b:property name="targetObject" ref="businessDataSource"/>
+        <b:property name="targetMethod" value="addConnectionProperty"/>
+        <b:property name="arguments">
+            <b:list>
+                <b:value>allowLoadLocalInfile</b:value>
+                <b:value>true</b:value>
+            </b:list>
+        </b:property>
+    </b:bean>
+
     <!-- scan for mappers and let them be autowired -->
     <bean class="org.mybatis.spring.mapper.MapperScannerConfigurer">
         <property name="basePackage" value="org.mskcc.cbio.portal.persistence,org.cbioportal.persistence.mybatis" />