fix critical and high vulnerabilities

cBioPortal · Jan 9, 2025 · 989c4c7 · 989c4c7
1 parent 6dc5fc7
commit 989c4c7
Show file tree

Hide file tree

Showing 4 changed files with 302 additions and 9 deletions.
diff --git a/pom.xml b/pom.xml
@@ -79,7 +79,7 @@
 
 
 		<!-- Third Party -->
-		<redisson.version>3.13.2</redisson.version>
+		<redisson.version>3.22.0</redisson.version>
 		<commons-math3.version>3.6.1</commons-math3.version>
 		<springdoc.version>2.2.0</springdoc.version>
 		<apache-commons-collections.version>4.4</apache-commons-collections.version>
@@ -93,13 +93,13 @@
 		<json_simple.version>1.1.1</json_simple.version>
 		<mongo_java_driver.version>3.12.14</mongo_java_driver.version>
 		<datumbox.version>0.8.2</datumbox.version>
-		<mysql_driver.version>8.0.33</mysql_driver.version>
 		<dasniko-testcontainer-keycloak.version>3.2.0</dasniko-testcontainer-keycloak.version>
 		<selenium_chrome_driver.version>3.14.0</selenium_chrome_driver.version>
         <selenium.version>4.17.0</selenium.version>
 		<sentry.version>7.1.0</sentry.version>
         <apache_httpclient.version>5.2.1</apache_httpclient.version>
         <clickhouse_testcontainer.version>1.19.7</clickhouse_testcontainer.version>
+        <bouncy_castle.version>1.78</bouncy_castle.version>
 
 
 		<!-- No sure what these are for -->
@@ -249,11 +249,6 @@
             <artifactId>jwks-rsa</artifactId>
             <version>0.22.1</version>
         </dependency>
-		<dependency>
-			<groupId>mysql</groupId>
-			<artifactId>mysql-connector-java</artifactId>
-			<version>${mysql_driver.version}</version>
-		</dependency>
 		<dependency>
 			<groupId>org.springframework.boot</groupId>
 			<artifactId>spring-boot-starter-thymeleaf</artifactId>
@@ -380,6 +375,36 @@
             <artifactId>spring-boot-testcontainers</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>commons-io</groupId>
+            <artifactId>commons-io</artifactId>
+            <version>2.18.0</version>
+        </dependency>
+        <dependency>
+            <groupId>com.nimbusds</groupId>
+            <artifactId>nimbus-jose-jwt</artifactId>
+            <version>9.37.2</version>
+        </dependency>
+        <dependency>
+            <groupId>org.bouncycastle</groupId>
+            <artifactId>bcpkix-jdk18on</artifactId>
+            <version>${bouncy_castle.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.bouncycastle</groupId>
+            <artifactId>bc-fips</artifactId>
+            <version>2.0.0</version>
+        </dependency>
+        <dependency>
+            <groupId>org.bouncycastle</groupId>
+            <artifactId>bcprov-jdk18on</artifactId>
+            <version>${bouncy_castle.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.bouncycastle</groupId>
+            <artifactId>bctls-jdk18on</artifactId>
+            <version>${bouncy_castle.version}</version>
+        </dependency>
     </dependencies>
 
     <dependencyManagement>

diff --git a/src/test/java/org/cbioportal/persistence/util/fakeclient/MockInMemoryRedissonClient.java b/src/test/java/org/cbioportal/persistence/util/fakeclient/MockInMemoryRedissonClient.java
@@ -4,6 +4,7 @@
 import org.redisson.api.redisnode.BaseRedisNodes;
 import org.redisson.api.redisnode.RedisNodes;
 import org.redisson.client.codec.Codec;
+import org.redisson.codec.JsonCodec;
 import org.redisson.config.Config;
 
 import java.util.concurrent.ConcurrentHashMap;
@@ -32,12 +33,12 @@ public RKeys getKeys() {
     }
 
     @Override
-    public <V> RTimeSeries<V> getTimeSeries(String s) {
+    public <V, L> RTimeSeries<V, L> getTimeSeries(String s) {
         throw new UnsupportedOperationException(); 
     }
 
     @Override
-    public <V> RTimeSeries<V> getTimeSeries(String s, Codec codec) {
+    public <V, L> RTimeSeries<V, L> getTimeSeries(String s, Codec codec) {
         throw new UnsupportedOperationException(); 
     }
 
@@ -51,6 +52,16 @@ public <K, V> RStream<K, V> getStream(String s, Codec codec) {
         throw new UnsupportedOperationException(); 
     }
 
+    @Override
+    public RSearch getSearch() {
+        throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public RSearch getSearch(Codec codec) {
+        throw new UnsupportedOperationException();
+    }
+
     @Override
     public RRateLimiter getRateLimiter(String s) {
         throw new UnsupportedOperationException(); 
@@ -116,6 +127,11 @@ public RBuckets getBuckets(Codec codec) {
         throw new UnsupportedOperationException(); 
     }
 
+    @Override
+    public <V> RJsonBucket<V> getJsonBucket(String name, JsonCodec<V> codec) {
+        throw new UnsupportedOperationException();
+    }
+
     @Override
     public <V> RHyperLogLog<V> getHyperLogLog(String s) {
         throw new UnsupportedOperationException(); 
@@ -221,6 +237,21 @@ public RLock getLock(String s) {
         throw new UnsupportedOperationException(); 
     }
 
+    @Override
+    public RLock getSpinLock(String s) {
+        throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public RLock getSpinLock(String s, LockOptions.BackOff backOff) {
+        throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public RFencedLock getFencedLock(String s) {
+        throw new UnsupportedOperationException();
+    }
+
     @Override
     public RLock getMultiLock(RLock... rLocks) {
         throw new UnsupportedOperationException(); 
@@ -281,6 +312,16 @@ public RLexSortedSet getLexSortedSet(String s) {
         throw new UnsupportedOperationException(); 
     }
 
+    @Override
+    public RShardedTopic getShardedTopic(String s) {
+        throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public RShardedTopic getShardedTopic(String s, Codec codec) {
+        throw new UnsupportedOperationException();
+    }
+
     @Override
     public RTopic getTopic(String s) {
         throw new UnsupportedOperationException(); 
@@ -291,6 +332,16 @@ public RTopic getTopic(String s, Codec codec) {
         throw new UnsupportedOperationException(); 
     }
 
+    @Override
+    public RReliableTopic getReliableTopic(String s) {
+        throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public RReliableTopic getReliableTopic(String s, Codec codec) {
+        throw new UnsupportedOperationException();
+    }
+
     @Override
     public RPatternTopic getPatternTopic(String s) {
         throw new UnsupportedOperationException(); 
@@ -456,6 +507,21 @@ public <V> RBloomFilter<V> getBloomFilter(String s, Codec codec) {
         throw new UnsupportedOperationException(); 
     }
 
+    @Override
+    public RIdGenerator getIdGenerator(String s) {
+        throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public RFunction getFunction() {
+        throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public RFunction getFunction(Codec codec) {
+        throw new UnsupportedOperationException();
+    }
+
     @Override
     public RScript getScript() {
         throw new UnsupportedOperationException(); 
@@ -526,6 +592,16 @@ public RLiveObjectService getLiveObjectService() {
         throw new UnsupportedOperationException(); 
     }
 
+    @Override
+    public RedissonRxClient rxJava() {
+        throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public RedissonReactiveClient reactive() {
+        throw new UnsupportedOperationException();
+    }
+
     @Override
     public void shutdown() {