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Upgrade to spring boot 3.4 (#11318)
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* upgrade to spring boot 3.4

* fix critical and high vulnerabilities

* fix vulnerability with commons-io

* fix mysql connector vulnerability

* fix security integration tests

* add back test scopes

* remove conflicting dependencies

---------

Co-authored-by: Bryan Lai <[email protected]>
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@gblaih
gblaih and Bryan Lai authored Jan 13, 2025
1 parent 3e67e8a commit 50f78d9
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Showing 8 changed files with 466 additions and 53 deletions.
27 changes: 16 additions & 11 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>3.1.4</version>
<version>3.4.1</version>
</parent>

<groupId>org.cbioportal</groupId>
Expand Down Expand Up @@ -38,6 +38,7 @@

<jackson.version>2.12.5</jackson.version>
<mysql-connector.version>8.0.28</mysql-connector.version>
<mysql.version>8.2.0</mysql.version>
<springfox.version>3.0.0</springfox.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
Expand Down Expand Up @@ -72,14 +73,14 @@

<!-- Unknown -->
<io.swagger.version>1.6.3</io.swagger.version>
<mybatis.starter.version>3.0.2</mybatis.starter.version>
<mybatis.starter.version>3.0.4</mybatis.starter.version>
<testcontainers.version>1.19.4</testcontainers.version>
<mockserver.version>5.15.0</mockserver.version>
<opensaml.version>4.1.1</opensaml.version>


<!-- 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>
Expand All @@ -93,13 +94,12 @@
<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 -->
Expand Down Expand Up @@ -211,6 +211,12 @@
<groupId>com.github.romain-warnan</groupId>
<artifactId>simple-java-bitly</artifactId>
<version>${simple_java_bitly.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.ehcache</groupId>
Expand Down Expand Up @@ -249,11 +255,11 @@
<artifactId>jwks-rsa</artifactId>
<version>0.22.1</version>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>${mysql_driver.version}</version>
</dependency>
<dependency>
<groupId>com.mysql</groupId>
<artifactId>mysql-connector-j</artifactId>
<version>${mysql.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-thymeleaf</artifactId>
Expand Down Expand Up @@ -351,7 +357,6 @@
<dependency>
<groupId>org.apache.httpcomponents.client5</groupId>
<artifactId>httpclient5</artifactId>
<version>${apache_httpclient.version}</version>
<scope>test</scope>
</dependency>

Expand Down
8 changes: 4 additions & 4 deletions src/main/resources/org/cbioportal/persistence/mybatis/ClinicalEventMapper.xml
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Expand Up @@ -228,9 +228,9 @@
clinical_event.EVENT_TYPE = #{element.eventType}
</if>
<if test="element.attributes != null and !element.attributes.isEmpty()">
(clinical_event.EVENT_TYPE, clinical_event_data.KEY, clinical_event_data.VALUE) IN
(CONCAT(clinical_event.EVENT_TYPE, '_', clinical_event_data.KEY, '_', clinical_event_data.VALUE)) IN
<foreach item="attribute" collection="element.attributes" open="(" separator="," close=")">
(#{element.eventType}, #{attribute.key}, #{attribute.value})
CONCAT(#{element.eventType}, '_', #{attribute.key}, '_', #{attribute.value})
</foreach>
</if>
</foreach>
Expand Down Expand Up @@ -291,9 +291,9 @@
clinical_event.EVENT_TYPE = #{element.eventType}
</if>
<if test="element.attributes != null and !element.attributes.isEmpty()">
(clinical_event.EVENT_TYPE, clinical_event_data.KEY) IN
(CONCAT(clinical_event.EVENT_TYPE, '_', clinical_event_data.KEY)) IN
<foreach item="attribute" collection="element.attributes" open="(" separator="," close=")">
(#{element.eventType}, #{attribute.key})
CONCAT(#{element.eventType}, '_', #{attribute.key})
</foreach>
</if>
</foreach>
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8 changes: 4 additions & 4 deletions src/test/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMyBatisRepositoryTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -181,16 +181,16 @@ public void fetchCopyNumberSegments() throws Exception {
studyIds, sampleIds, "3", "SUMMARY");

Assert.assertEquals(3, result0.size());
Assert.assertEquals("TCGA-A1-B0SO-01", result0.get(0).getSampleStableId());
Assert.assertEquals("TCGA-A1-A0SB-01", result0.get(0).getSampleStableId());
Assert.assertEquals("TCGA-A1-A0SB-01", result0.get(1).getSampleStableId());
Assert.assertEquals("TCGA-A1-A0SB-01", result0.get(2).getSampleStableId());
Assert.assertEquals("TCGA-A1-B0SO-01", result0.get(2).getSampleStableId());

Assert.assertEquals(1, result1.size());
Assert.assertEquals("TCGA-A1-A0SB-01", result1.get(0).getSampleStableId());

Assert.assertEquals(2, result2.size());
Assert.assertEquals("TCGA-A1-B0SO-01", result2.get(0).getSampleStableId());
Assert.assertEquals("TCGA-A1-A0SB-01", result2.get(1).getSampleStableId());
Assert.assertEquals("TCGA-A1-A0SB-01", result2.get(0).getSampleStableId());
Assert.assertEquals("TCGA-A1-B0SO-01", result2.get(1).getSampleStableId());

Assert.assertEquals(0, result3.size());
}
Expand Down
80 changes: 78 additions & 2 deletions src/test/java/org/cbioportal/persistence/util/fakeclient/MockInMemoryRedissonClient.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down Expand Up @@ -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();
}

Expand All @@ -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();
Expand Down Expand Up @@ -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();
Expand Down Expand Up @@ -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();
Expand Down Expand Up @@ -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();
Expand All @@ -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();
Expand Down Expand Up @@ -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();
Expand Down Expand Up @@ -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() {

Expand Down
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