The dreaded Java SpringBoot app not connecting to MySQL with Docker-compose java.net.ConnectException: Connection refused

I have been struggling with the following issue – the dreaded Java SpringBoot app not connecting to MySQL with docker compose exceptions:

com.mysql.cj.jdbc.exceptions.CommunicationsException: Communications link failure

JDBCConnectionException: Unable to open JDBC Connection for DDL execution

java.net.ConnectException: Connection refused

The app works fine on its own, but it can’t seem to connect to mysql once I get it in Docker. I think I have all parameters correct, what am I missing?

Platform:

MacOS Mojave 10.14.6
---
Docker version 19.03.13, build 4484c46d9d
docker-compose version 1.27.4, build 40524192
---
mysql  Ver 8.0.21 for osx10.14 on x86_64 (Homebrew)
---
openjdk 11.0.8 2020-07-14
OpenJDK Runtime Environment AdoptOpenJDK (build 11.0.8+10)
OpenJDK 64-Bit Server VM AdoptOpenJDK (build 11.0.8+10, mixed mode)
---
Spring CLI v2.3.4.RELEASE
---
Apache Maven 3.5.4 (1edded0938998edf8bf061f1ceb3cfdeccf443fe; 2018-06-17T21:33:14+03:00)
Maven home: /usr/local/Cellar/maven@3.5/3.5.4_1/libexec
Java version: 11.0.8, vendor: AdoptOpenJDK, runtime: /Library/Java/JavaVirtualMachines/adoptopenjdk-11.jdk/Contents/Home
Default locale: en_GB, platform encoding: UTF-8
OS name: "mac os x", version: "10.14.6", arch: "x86_64", family: "mac"

JavaScript
​x
 
MacOS Mojave 10.14.6---Docker version 19.03.13, build 4484c46d9ddocker-compose version 1.27.4, build 40524192---mysql  Ver 8.0.21 for osx10.14 on x86_64 (Homebrew)---openjdk 11.0.8 2020-07-14OpenJDK Runtime Environment AdoptOpenJDK (build 11.0.8+10)OpenJDK 64-Bit Server VM AdoptOpenJDK (build 11.0.8+10, mixed mode)---Spring CLI v2.3.4.RELEASE---Apache Maven 3.5.4 (1edded0938998edf8bf061f1ceb3cfdeccf443fe; 2018-06-17T21:33:14+03:00)Maven home: /usr/local/Cellar/maven@3.5/3.5.4_1/libexecJava version: 11.0.8, vendor: AdoptOpenJDK, runtime: /Library/Java/JavaVirtualMachines/adoptopenjdk-11.jdk/Contents/HomeDefault locale: en_GB, platform encoding: UTF-8OS name: "mac os x", version: "10.14.6", arch: "x86_64", family: "mac"​

Here is the whole codebase: Codebase

Run with command:

docker-compose up --build --remove-orphans

JavaScript
 
docker-compose up --build --remove-orphans​

My docker-compose.yml (The commented out stuff is things I tried):

version: "3.8"
services:
  genesysmysql:
    container_name: genesysmysql
#    container_name: genesysmysql_container
    image: "mysql:8.0.21"
    restart: always
    environment:
      - MYSQL_ROOT_PASSWORD=root
      - MYSQL_DATABASE=db_example
      - MYSQL_USER=springuser
      - MYSQL_PASSWORD=ThePassword
    ports:
      - 3306:3306
    volumes:
      - ./setup.sql:/docker-entrypoint-initdb.d/setup.sql:ro
    healthcheck:
      test: [ "CMD", "mysqladmin" ,"ping", "-h", "localhost" ]
      timeout: 20s
      retries: 20
  genesys:
    build: .
    ports:
      - 8080:8080
    depends_on:
      genesysmysql:
        condition: service_healthy
    environment:
      - spring.datasource.jdbc-url=jdbc:genesysmysql://db_example:3306?useSSL=false&allowPublicKeyRetrieval=true&autoReconnect=true
#      - spring.datasource.jdbc-url=jdbc:genesysmysql://db_example:3306?useSSL=false&allowPublicKeyRetrieval=true&serverTimezone=UTC&autoReconnect=true
      - spring.datasource.driver-class-name=com.mysql.cj.jdbc.Driver
#      - spring.datasource.username=root
#      - spring.datasource.password=root
#      - spring.datasource.username=springuser
#      - spring.datasource.password=ThePassword
#      - spring.jpa.hibernate.ddl-auto=create-drop
      - spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.MySQL5Dialect
#      - spring.data.jpa.repositories.enabled=true
#      - spring.jpa.database-platform=org.hibernate.dialect.MySQL5Dialect
#      - spring.jpa.generate-ddl=true

JavaScript
 
version: "3.8"services:  genesysmysql:    container_name: genesysmysql#    container_name: genesysmysql_container    image: "mysql:8.0.21"    restart: always    environment:      - MYSQL_ROOT_PASSWORD=root      - MYSQL_DATABASE=db_example      - MYSQL_USER=springuser      - MYSQL_PASSWORD=ThePassword    ports:      - 3306:3306    volumes:      - ./setup.sql:/docker-entrypoint-initdb.d/setup.sql:ro    healthcheck:      test: [ "CMD", "mysqladmin" ,"ping", "-h", "localhost" ]      timeout: 20s      retries: 20  genesys:    build: .    ports:      - 8080:8080    depends_on:      genesysmysql:        condition: service_healthy    environment:      - spring.datasource.jdbc-url=jdbc:genesysmysql://db_example:3306?useSSL=false&allowPublicKeyRetrieval=true&autoReconnect=true#      - spring.datasource.jdbc-url=jdbc:genesysmysql://db_example:3306?useSSL=false&allowPublicKeyRetrieval=true&serverTimezone=UTC&autoReconnect=true      - spring.datasource.driver-class-name=com.mysql.cj.jdbc.Driver#      - spring.datasource.username=root#      - spring.datasource.password=root#      - spring.datasource.username=springuser#      - spring.datasource.password=ThePassword#      - spring.jpa.hibernate.ddl-auto=create-drop      - spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.MySQL5Dialect#      - spring.data.jpa.repositories.enabled=true#      - spring.jpa.database-platform=org.hibernate.dialect.MySQL5Dialect#      - spring.jpa.generate-ddl=true​

My setup.sql script:

CREATE DATABASE db_example;
CREATE USER 'springuser'@'%' IDENTIFIED BY 'ThePassword';
GRANT ALL ON db_example.* to 'springuser'@'%';
GRANT ALL ON db_example.* TO 'springuser'@'localhost';
GRANT ALL ON db_example.* TO 'springuser'@'genesysmysql_container';
GRANT ALL ON db_example.* TO 'springuser'@'genesysmysql';

JavaScript
 
CREATE DATABASE db_example;CREATE USER 'springuser'@'%' IDENTIFIED BY 'ThePassword';GRANT ALL ON db_example.* to 'springuser'@'%';GRANT ALL ON db_example.* TO 'springuser'@'localhost';GRANT ALL ON db_example.* TO 'springuser'@'genesysmysql_container';GRANT ALL ON db_example.* TO 'springuser'@'genesysmysql';​

My dockerfile:

FROM adoptopenjdk/openjdk11:alpine
MAINTAINER  atkuzmanov <https://github.com/atkuzmanov>
RUN addgroup -S spring && adduser -S spring -G spring
USER spring:spring
ARG JAR_FILE=target/*.jar
COPY ${JAR_FILE} app.jar
EXPOSE 8080
ENTRYPOINT ["java","-jar","/app.jar"]

JavaScript
 
FROM adoptopenjdk/openjdk11:alpineMAINTAINER  atkuzmanov <https://github.com/atkuzmanov>RUN addgroup -S spring && adduser -S spring -G springUSER spring:springARG JAR_FILE=target/*.jarCOPY ${JAR_FILE} app.jarEXPOSE 8080ENTRYPOINT ["java","-jar","/app.jar"]​

My application.properties file:

### Spring properties
spring.application.name=@project.name@
#spring.output.ansi.console-available=true
#server.port=8080
spring.output.ansi.enabled=ALWAYS

### Spring banner properties
#spring.banner.location=classpath:banner.txt
#spring.main.banner-mode=off
info.app.name=@project.name@
info.app.version=@project.version@
info.app.url=@project.url@

### Spring Actuator properties
## Do not expose or enable the 'shutdown' option in a public production application.
#management.endpoint.shutdown.enabled=true
management.endpoints.web.exposure.include=health,info,httptrace

### Spring Devtools properties
#spring.devtools.add-properties=false
#spring.devtools.restart.log-condition-evaluation-delta=false
#spring.devtools.restart.enabled=false
#spring.devtools.livereload.enabled=false

### Spring logging properties
## Change logging levels as appropriate when debugging
logging.level.=WARN
logging.level.customLogbackLevel=INFO
logging.level.org.springframework=WARN
logging.level.org.springframework.web.servlet.=ERROR
logging.level.org.hibernate=ERROR
logging.level.org.apache.catalina.core.ContainerBase.=WARN

### Spring Distributed Tracing properties
## Zipkin properties
spring.zipkin.enabled=true
spring.zipkin.base-url=http://127.0.0.1:9411/
## Sleuth properties
spring.sleuth.enabled=true
spring.sleuth.sampler.percentage=0.5
#spring.sleuth.web.skipPattern=(^cleanup.*|.+favicon.*)

### Spring Data properties
## These are just to get things started, should be changed afterwards.
#spring.jpa.hibernate.ddl-auto=none
spring.jpa.hibernate.ddl-auto=update
spring.datasource.url=jdbc:mysql://${MYSQL_HOST:localhost}:3306/db_example?useSSL=false&allowPublicKeyRetrieval=true
spring.datasource.username=springuser
spring.datasource.password=ThePassword
#spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.MySQL5

### Spring Open Session properties
### Warning message by default:
## "spring.jpa.open-in-view is enabled by default.
## Therefore, database queries may be performed during view rendering.
## Explicitly configure spring.jpa.open-in-view to disable this warning"
## See:
## RE: spring.jpa.open-in-view Warning
## - <https://stackoverflow.com/questions/30549489/what-is-this-spring-jpa-open-in-view-true-property-in-spring-boot>
## - <https://www.baeldung.com/spring-open-session-in-view>
spring.jpa.open-in-view=true

### Spring Thymeleaf properties
spring.thymeleaf.cache=false

JavaScript
 
### Spring propertiesspring.application.name=@project.name@#spring.output.ansi.console-available=true#server.port=8080spring.output.ansi.enabled=ALWAYS​### Spring banner properties#spring.banner.location=classpath:banner.txt#spring.main.banner-mode=offinfo.app.name=@project.name@info.app.version=@project.version@info.app.url=@project.url@​### Spring Actuator properties## Do not expose or enable the 'shutdown' option in a public production application.#management.endpoint.shutdown.enabled=truemanagement.endpoints.web.exposure.include=health,info,httptrace​### Spring Devtools properties#spring.devtools.add-properties=false#spring.devtools.restart.log-condition-evaluation-delta=false#spring.devtools.restart.enabled=false#spring.devtools.livereload.enabled=false​### Spring logging properties## Change logging levels as appropriate when debugginglogging.level.=WARNlogging.level.customLogbackLevel=INFOlogging.level.org.springframework=WARNlogging.level.org.springframework.web.servlet.=ERRORlogging.level.org.hibernate=ERRORlogging.level.org.apache.catalina.core.ContainerBase.=WARN​### Spring Distributed Tracing properties## Zipkin propertiesspring.zipkin.enabled=truespring.zipkin.base-url=http://127.0.0.1:9411/## Sleuth propertiesspring.sleuth.enabled=truespring.sleuth.sampler.percentage=0.5#spring.sleuth.web.skipPattern=(^cleanup.*|.+favicon.*)​### Spring Data properties## These are just to get things started, should be changed afterwards.#spring.jpa.hibernate.ddl-auto=nonespring.jpa.hibernate.ddl-auto=updatespring.datasource.url=jdbc:mysql://${MYSQL_HOST:localhost}:3306/db_example?useSSL=false&allowPublicKeyRetrieval=truespring.datasource.username=springuserspring.datasource.password=ThePassword#spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.MySQL5​### Spring Open Session properties### Warning message by default:## "spring.jpa.open-in-view is enabled by default.## Therefore, database queries may be performed during view rendering.## Explicitly configure spring.jpa.open-in-view to disable this warning"## See:## RE: spring.jpa.open-in-view Warning## - <https://stackoverflow.com/questions/30549489/what-is-this-spring-jpa-open-in-view-true-property-in-spring-boot>## - <https://www.baeldung.com/spring-open-session-in-view>spring.jpa.open-in-view=true​### Spring Thymeleaf propertiesspring.thymeleaf.cache=false​

Here are the exception messages:

Exception 1: Exception 1
Eception 2: Exception 2
Exception 3: Exception 3
Exception 4, which encapsulates all of them: Exception 4

{
  "app": "GeneSys",
  "logMsgId": "f7b6c3cc-0dce-4eb6-b6c3-cc0dce1eb69c",
  "@timestamp": "2020-11-11T11:20:31.822Z",
  "@version": "1",
  "logger": "org.springframework.boot.SpringApplication",
  "level": "ERROR",
  "thread": "main",
  "stackTrace": "org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'timestampRepository' defined in com.atkuzmanov.genesys.dao.TimestampRepository defined in @EnableJpaRepositories declared on JpaRepositoriesRegistrar.EnableJpaRepositoriesConfiguration: Cannot resolve reference to bean 'jpaMappingContext' while setting bean property 'mappingContext'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'jpaMappingContext': Invocation of init method failed; nested exception is javax.persistence.PersistenceException: [PersistenceUnit: default] Unable to build Hibernate SessionFactory; nested exception is org.hibernate.exception.JDBCConnectionException: Unable to open JDBC Connection for DDL execution
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:342)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:113)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1697)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1442)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:593)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:516)
    at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:324)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:322)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.getBeansOfType(DefaultListableBeanFactory.java:624)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.getBeansOfType(DefaultListableBeanFactory.java:612)
    at org.springframework.data.repository.config.DeferredRepositoryInitializationListener.onApplicationEvent(DeferredRepositoryInitializationListener.java:51)
    at org.springframework.data.repository.config.DeferredRepositoryInitializationListener.onApplicationEvent(DeferredRepositoryInitializationListener.java:36)
    at org.springframework.context.event.SimpleApplicationEventMulticaster.doInvokeListener(SimpleApplicationEventMulticaster.java:172)
    at org.springframework.context.event.SimpleApplicationEventMulticaster.invokeListener(SimpleApplicationEventMulticaster.java:165)
    at org.springframework.context.event.SimpleApplicationEventMulticaster.multicastEvent(SimpleApplicationEventMulticaster.java:139)
    at org.springframework.context.support.AbstractApplicationContext.publishEvent(AbstractApplicationContext.java:404)
    at org.springframework.context.support.AbstractApplicationContext.publishEvent(AbstractApplicationContext.java:361)
    at org.springframework.context.support.AbstractApplicationContext.finishRefresh(AbstractApplicationContext.java:898)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:554)
    at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:143)
    at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:758)
    at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:750)
    at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:397)
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:315)
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1237)
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1226)
    at com.atkuzmanov.genesys.GenesysApplication.main(GenesysApplication.java:15)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:49)
    at org.springframework.boot.loader.Launcher.launch(Launcher.java:107)
    at org.springframework.boot.loader.Launcher.launch(Launcher.java:58)
    at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:88)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'jpaMappingContext': Invocation of init method failed; nested exception is javax.persistence.PersistenceException: [PersistenceUnit: default] Unable to build Hibernate SessionFactory; nested exception is org.hibernate.exception.JDBCConnectionException: Unable to open JDBC Connection for DDL execution
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1794)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:594)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:516)
    at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:324)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:322)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:330)
    ... 36 common frames omitted
Caused by: javax.persistence.PersistenceException: [PersistenceUnit: default] Unable to build Hibernate SessionFactory; nested exception is org.hibernate.exception.JDBCConnectionException: Unable to open JDBC Connection for DDL execution
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.buildNativeEntityManagerFactory(AbstractEntityManagerFactoryBean.java:403)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
    at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: org.hibernate.exception.JDBCConnectionException: Unable to open JDBC Connection for DDL execution
    at org.hibernate.exception.internal.SQLStateConversionDelegate.convert(SQLStateConversionDelegate.java:112)
    at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:42)
    at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:113)
    at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:99)
    at org.hibernate.resource.transaction.backend.jdbc.internal.DdlTransactionIsolatorNonJtaImpl.getIsolatedConnection(DdlTransactionIsolatorNonJtaImpl.java:69)
    at org.hibernate.tool.schema.internal.exec.ImprovedExtractionContextImpl.getJdbcConnection(ImprovedExtractionContextImpl.java:60)
    at org.hibernate.tool.schema.internal.exec.ImprovedExtractionContextImpl.getJdbcDatabaseMetaData(ImprovedExtractionContextImpl.java:67)
    at org.hibernate.tool.schema.extract.internal.InformationExtractorJdbcDatabaseMetaDataImpl.getTables(InformationExtractorJdbcDatabaseMetaDataImpl.java:333)
    at org.hibernate.tool.schema.extract.internal.DatabaseInformationImpl.getTablesInformation(DatabaseInformationImpl.java:120)
    at org.hibernate.tool.schema.internal.GroupedSchemaMigratorImpl.performTablesMigration(GroupedSchemaMigratorImpl.java:65)
    at org.hibernate.tool.schema.internal.AbstractSchemaMigrator.performMigration(AbstractSchemaMigrator.java:207)
    at org.hibernate.tool.schema.internal.AbstractSchemaMigrator.doMigration(AbstractSchemaMigrator.java:114)
    at org.hibernate.tool.schema.spi.SchemaManagementToolCoordinator.performDatabaseAction(SchemaManagementToolCoordinator.java:184)
    at org.hibernate.tool.schema.spi.SchemaManagementToolCoordinator.process(SchemaManagementToolCoordinator.java:73)
    at org.hibernate.internal.SessionFactoryImpl.<init>(SessionFactoryImpl.java:316)
    at org.hibernate.boot.internal.SessionFactoryBuilderImpl.build(SessionFactoryBuilderImpl.java:469)
    at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.build(EntityManagerFactoryBuilderImpl.java:1259)
    at org.springframework.orm.jpa.vendor.SpringHibernateJpaPersistenceProvider.createContainerEntityManagerFactory(SpringHibernateJpaPersistenceProvider.java:58)
    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:365)
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.buildNativeEntityManagerFactory(AbstractEntityManagerFactoryBean.java:391)
    ... 4 common frames omitted
Caused by: com.mysql.cj.jdbc.exceptions.CommunicationsException: Communications link failure

The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.
    at com.mysql.cj.jdbc.exceptions.SQLError.createCommunicationsException(SQLError.java:174)
    at com.mysql.cj.jdbc.exceptions.SQLExceptionsMapping.translateException(SQLExceptionsMapping.java:64)
    at com.mysql.cj.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:836)
    at com.mysql.cj.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:456)
    at com.mysql.cj.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:246)
    at com.mysql.cj.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:197)
    at com.zaxxer.hikari.util.DriverDataSource.getConnection(DriverDataSource.java:138)
    at com.zaxxer.hikari.pool.PoolBase.newConnection(PoolBase.java:358)
    at com.zaxxer.hikari.pool.PoolBase.newPoolEntry(PoolBase.java:206)
    at com.zaxxer.hikari.pool.HikariPool.createPoolEntry(HikariPool.java:477)
    at com.zaxxer.hikari.pool.HikariPool.checkFailFast(HikariPool.java:560)
    at com.zaxxer.hikari.pool.HikariPool.<init>(HikariPool.java:115)
    at com.zaxxer.hikari.HikariDataSource.getConnection(HikariDataSource.java:112)
    at org.hibernate.engine.jdbc.connections.internal.DatasourceConnectionProviderImpl.getConnection(DatasourceConnectionProviderImpl.java:122)
    at org.hibernate.engine.jdbc.env.internal.JdbcEnvironmentInitiator$ConnectionProviderJdbcConnectionAccess.obtainConnection(JdbcEnvironmentInitiator.java:180)
    at org.hibernate.resource.transaction.backend.jdbc.internal.DdlTransactionIsolatorNonJtaImpl.getIsolatedConnection(DdlTransactionIsolatorNonJtaImpl.java:43)
    ... 19 common frames omitted
Caused by: com.mysql.cj.exceptions.CJCommunicationsException: Communications link failure

The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
    at com.mysql.cj.exceptions.ExceptionFactory.createException(ExceptionFactory.java:61)
    at com.mysql.cj.exceptions.ExceptionFactory.createException(ExceptionFactory.java:105)
    at com.mysql.cj.exceptions.ExceptionFactory.createException(ExceptionFactory.java:151)
    at com.mysql.cj.exceptions.ExceptionFactory.createCommunicationsException(ExceptionFactory.java:167)
    at com.mysql.cj.protocol.a.NativeSocketConnection.connect(NativeSocketConnection.java:91)
    at com.mysql.cj.NativeSession.connect(NativeSession.java:144)
    at com.mysql.cj.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:956)
    at com.mysql.cj.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:826)
    ... 32 common frames omitted
Caused by: java.net.ConnectException: Connection refused (Connection refused)
    at java.base/java.net.PlainSocketImpl.socketConnect(Native Method)
    at java.base/java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:399)
    at java.base/java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:242)
    at java.base/java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:224)
    at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:403)
    at java.base/java.net.Socket.connect(Socket.java:609)
    at com.mysql.cj.protocol.StandardSocketFactory.connect(StandardSocketFactory.java:155)
    at com.mysql.cj.protocol.a.NativeSocketConnection.connect(NativeSocketConnection.java:65)
    ... 35 common frames omitted
",
  "message": "Application run failed",
  "method": "reportFailure",
  "class": "org.springframework.boot.SpringApplication"
}

JavaScript
 
{  "app": "GeneSys",  "logMsgId": "f7b6c3cc-0dce-4eb6-b6c3-cc0dce1eb69c",  "@timestamp": "2020-11-11T11:20:31.822Z",  "@version": "1",  "logger": "org.springframework.boot.SpringApplication",  "level": "ERROR",  "thread": "main",  "stackTrace": "org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'timestampRepository' defined in com.atkuzmanov.genesys.dao.TimestampRepository defined in @EnableJpaRepositories declared on JpaRepositoriesRegistrar.EnableJpaRepositoriesConfiguration: Cannot resolve reference to bean 'jpaMappingContext' while setting bean property 'mappingContext'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'jpaMappingContext': Invocation of init method failed; nested exception is javax.persistence.PersistenceException: [PersistenceUnit: default] Unable to build Hibernate SessionFactory; nested exception is org.hibernate.exception.JDBCConnectionException: Unable to open JDBC Connection for DDL execution    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:342)    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:113)    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1697)    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1442)    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:593)    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:516)    at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:324)    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:322)    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)    at org.springframework.beans.factory.support.DefaultListableBeanFactory.getBeansOfType(DefaultListableBeanFactory.java:624)    at org.springframework.beans.factory.support.DefaultListableBeanFactory.getBeansOfType(DefaultListableBeanFactory.java:612)    at org.springframework.data.repository.config.DeferredRepositoryInitializationListener.onApplicationEvent(DeferredRepositoryInitializationListener.java:51)    at org.springframework.data.repository.config.DeferredRepositoryInitializationListener.onApplicationEvent(DeferredRepositoryInitializationListener.java:36)    at org.springframework.context.event.SimpleApplicationEventMulticaster.doInvokeListener(SimpleApplicationEventMulticaster.java:172)    at org.springframework.context.event.SimpleApplicationEventMulticaster.invokeListener(SimpleApplicationEventMulticaster.java:165)    at org.springframework.context.event.SimpleApplicationEventMulticaster.multicastEvent(SimpleApplicationEventMulticaster.java:139)    at org.springframework.context.support.AbstractApplicationContext.publishEvent(AbstractApplicationContext.java:404)    at org.springframework.context.support.AbstractApplicationContext.publishEvent(AbstractApplicationContext.java:361)    at org.springframework.context.support.AbstractApplicationContext.finishRefresh(AbstractApplicationContext.java:898)    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:554)    at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:143)    at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:758)    at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:750)    at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:397)    at org.springframework.boot.SpringApplication.run(SpringApplication.java:315)    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1237)    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1226)    at com.atkuzmanov.genesys.GenesysApplication.main(GenesysApplication.java:15)    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)    at java.base/java.lang.reflect.Method.invoke(Method.java:566)    at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:49)    at org.springframework.boot.loader.Launcher.launch(Launcher.java:107)    at org.springframework.boot.loader.Launcher.launch(Launcher.java:58)    at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:88)Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'jpaMappingContext': Invocation of init method failed; nested exception is javax.persistence.PersistenceException: [PersistenceUnit: default] Unable to build Hibernate SessionFactory; nested exception is org.hibernate.exception.JDBCConnectionException: Unable to open JDBC Connection for DDL execution    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1794)    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:594)    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:516)    at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:324)    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:322)    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:330)    ... 36 common frames omittedCaused by: javax.persistence.PersistenceException: [PersistenceUnit: default] Unable to build Hibernate SessionFactory; nested exception is org.hibernate.exception.JDBCConnectionException: Unable to open JDBC Connection for DDL execution    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.buildNativeEntityManagerFactory(AbstractEntityManagerFactoryBean.java:403)    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)    at java.base/java.lang.Thread.run(Thread.java:834)Caused by: org.hibernate.exception.JDBCConnectionException: Unable to open JDBC Connection for DDL execution    at org.hibernate.exception.internal.SQLStateConversionDelegate.convert(SQLStateConversionDelegate.java:112)    at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:42)    at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:113)    at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:99)    at org.hibernate.resource.transaction.backend.jdbc.internal.DdlTransactionIsolatorNonJtaImpl.getIsolatedConnection(DdlTransactionIsolatorNonJtaImpl.java:69)    at org.hibernate.tool.schema.internal.exec.ImprovedExtractionContextImpl.getJdbcConnection(ImprovedExtractionContextImpl.java:60)    at org.hibernate.tool.schema.internal.exec.ImprovedExtractionContextImpl.getJdbcDatabaseMetaData(ImprovedExtractionContextImpl.java:67)    at org.hibernate.tool.schema.extract.internal.InformationExtractorJdbcDatabaseMetaDataImpl.getTables(InformationExtractorJdbcDatabaseMetaDataImpl.java:333)    at org.hibernate.tool.schema.extract.internal.DatabaseInformationImpl.getTablesInformation(DatabaseInformationImpl.java:120)    at org.hibernate.tool.schema.internal.GroupedSchemaMigratorImpl.performTablesMigration(GroupedSchemaMigratorImpl.java:65)    at org.hibernate.tool.schema.internal.AbstractSchemaMigrator.performMigration(AbstractSchemaMigrator.java:207)    at org.hibernate.tool.schema.internal.AbstractSchemaMigrator.doMigration(AbstractSchemaMigrator.java:114)    at org.hibernate.tool.schema.spi.SchemaManagementToolCoordinator.performDatabaseAction(SchemaManagementToolCoordinator.java:184)    at org.hibernate.tool.schema.spi.SchemaManagementToolCoordinator.process(SchemaManagementToolCoordinator.java:73)    at org.hibernate.internal.SessionFactoryImpl.<init>(SessionFactoryImpl.java:316)    at org.hibernate.boot.internal.SessionFactoryBuilderImpl.build(SessionFactoryBuilderImpl.java:469)    at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.build(EntityManagerFactoryBuilderImpl.java:1259)    at org.springframework.orm.jpa.vendor.SpringHibernateJpaPersistenceProvider.createContainerEntityManagerFactory(SpringHibernateJpaPersistenceProvider.java:58)    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:365)    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.buildNativeEntityManagerFactory(AbstractEntityManagerFactoryBean.java:391)    ... 4 common frames omittedCaused by: com.mysql.cj.jdbc.exceptions.CommunicationsException: Communications link failure​The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.    at com.mysql.cj.jdbc.exceptions.SQLError.createCommunicationsException(SQLError.java:174)    at com.mysql.cj.jdbc.exceptions.SQLExceptionsMapping.translateException(SQLExceptionsMapping.java:64)    at com.mysql.cj.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:836)    at com.mysql.cj.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:456)    at com.mysql.cj.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:246)    at com.mysql.cj.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:197)    at com.zaxxer.hikari.util.DriverDataSource.getConnection(DriverDataSource.java:138)    at com.zaxxer.hikari.pool.PoolBase.newConnection(PoolBase.java:358)    at com.zaxxer.hikari.pool.PoolBase.newPoolEntry(PoolBase.java:206)    at com.zaxxer.hikari.pool.HikariPool.createPoolEntry(HikariPool.java:477)    at com.zaxxer.hikari.pool.HikariPool.checkFailFast(HikariPool.java:560)    at com.zaxxer.hikari.pool.HikariPool.<init>(HikariPool.java:115)    at com.zaxxer.hikari.HikariDataSource.getConnection(HikariDataSource.java:112)    at org.hibernate.engine.jdbc.connections.internal.DatasourceConnectionProviderImpl.getConnection(DatasourceConnectionProviderImpl.java:122)    at org.hibernate.engine.jdbc.env.internal.JdbcEnvironmentInitiator$ConnectionProviderJdbcConnectionAccess.obtainConnection(JdbcEnvironmentInitiator.java:180)    at org.hibernate.resource.transaction.backend.jdbc.internal.DdlTransactionIsolatorNonJtaImpl.getIsolatedConnection(DdlTransactionIsolatorNonJtaImpl.java:43)    ... 19 common frames omittedCaused by: com.mysql.cj.exceptions.CJCommunicationsException: Communications link failure​The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)    at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)    at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)    at com.mysql.cj.exceptions.ExceptionFactory.createException(ExceptionFactory.java:61)    at com.mysql.cj.exceptions.ExceptionFactory.createException(ExceptionFactory.java:105)    at com.mysql.cj.exceptions.ExceptionFactory.createException(ExceptionFactory.java:151)    at com.mysql.cj.exceptions.ExceptionFactory.createCommunicationsException(ExceptionFactory.java:167)    at com.mysql.cj.protocol.a.NativeSocketConnection.connect(NativeSocketConnection.java:91)    at com.mysql.cj.NativeSession.connect(NativeSession.java:144)    at com.mysql.cj.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:956)    at com.mysql.cj.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:826)    ... 32 common frames omittedCaused by: java.net.ConnectException: Connection refused (Connection refused)    at java.base/java.net.PlainSocketImpl.socketConnect(Native Method)    at java.base/java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:399)    at java.base/java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:242)    at java.base/java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:224)    at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:403)    at java.base/java.net.Socket.connect(Socket.java:609)    at com.mysql.cj.protocol.StandardSocketFactory.connect(StandardSocketFactory.java:155)    at com.mysql.cj.protocol.a.NativeSocketConnection.connect(NativeSocketConnection.java:65)    ... 35 common frames omitted",  "message": "Application run failed",  "method": "reportFailure",  "class": "org.springframework.boot.SpringApplication"}​

Answer

To fix it you just need to change parameter spring.datasource.jdbc-url to spring.datasource.url and connection string to jdbc:mysql://genesysmysql:3306/db_example?useSSL=false&allowPublicKeyRetrieval=true&autoReconnect=true. Your connection string has an error.

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Answer