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Upgrade to spring boot 3.4 #11318

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merged 7 commits into from
Jan 13, 2025
Merged

Upgrade to spring boot 3.4 #11318

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d52e31d
upgrade to spring boot 3.4
Jan 2, 2025
49b557c
fix critical and high vulnerabilities
Jan 9, 2025
ad2b9de
fix vulnerability with commons-io
Jan 9, 2025
a1d106a
fix mysql connector vulnerability
Jan 9, 2025
2f2f5ad
fix security integration tests
Jan 10, 2025
169cba5
add back test scopes
Jan 13, 2025
fbde89a
remove conflicting dependencies
Jan 13, 2025
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63 changes: 52 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>
Comment on lines +214 to +219
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Same as below are these test deps?
test

</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>
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</dependency>

Expand Down Expand Up @@ -380,6 +385,42 @@
<artifactId>spring-boot-testcontainers</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.velocity</groupId>
<artifactId>velocity-engine-core</artifactId>
<version>2.4.1</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.18.0</version>
<scope>test</scope>
</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>
Expand Down
8 changes: 4 additions & 4 deletions src/main/resources/org/cbioportal/persistence/mybatis/ClinicalEventMapper.xml
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Original file line number Diff line number Diff line change
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>
Expand Down
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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