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an entity class mapped to a mysql table and a UserRepository class(annotated with @Repository). I am trying to inject the crudrepository class via @Autowire annotation, but spring is having difficulty creating the datasource for it because it cannot find the mysql driver. What confuses me is that I have the mysql dependency in maven and I am deploying this on a glassfish 4 server, but Spring is trying to use apache tomcat to connect to the database. Below is my stack trace, code snippets, and mysql-connector:

Relevant Stack Trace (inner exception)

Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.apache.tomcat.jdbc.pool.DataSource]: Factory method 'dataSource' threw exception; nested exception is java.lang.IllegalStateException: Cannot load driver class: com.mysql.jdbc.driver
at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:189) ~[spring-beans-4.3.13.RELEASE.jar:4.3.13.RELEASE]
at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:588) ~[spring-beans-4.3.13.RELEASE.jar:4.3.13.RELEASE]
... 62 common frames omitted
Caused by: java.lang.IllegalStateException: Cannot load driver class: com.mysql.jdbc.driver
notice how this is trying to use org.apache.tomcat to create datasource, even though I am using a glassfish server.  Does this matter?
Source Code: the first relevant exception occurs when spring tries to inject the datasource bean that is a parameter to this method and can't create it
@Configuration
@EnableAutoConfiguration
public class AppConfigUtil {
@Autowired
@Bean 
public EntityManagerFactory entityManagerFactory(DataSource dataSource) { 
    LocalContainerEntityManagerFactoryBean bean = new LocalContainerEntityManagerFactoryBean(); 
    bean.setPackagesToScan("com.connor"); 
    bean.setDataSource(dataSource); 
    return bean.getObject(); 
Maven (pom.xml) for mysql jar:
    <!-- https://mvnrepository.com/artifact/mysql/mysql-connector-java -->
    <dependency>
        <groupId>mysql</groupId>
        <artifactId>mysql-connector-java</artifactId>
    </dependency>
application.properties: this is the entirety of my application.properties file spring uses to generate datasource
spring.datasource.url=jdbc:mysql://localhost:3307/craigslist
spring.datasource.username=dbadmin
spring.datasource.password=password
spring.datasource.driver-class-name=com.mysql.jdbc.driver
hibernate.dialect=org.hibernate.dialect.MySQLDialect
hibernate.show_sql=true
hibernate.format_sql=true
Here is picture of my maven dependencies: the mysql jar is present:
downloaded maven dependencies: including mysql jar
Any ideas on how to fix this?
                You don't need the AppConfigUtil Spring Boot configures all that for you. You don't need the spring.datasource.driver-class-name Spring (and hibernate) will automatically know the driver to load. Also the driver should be com.mysql.cj.jdbc.Driver and not com.mysql.jdbc.driver.
– M. Deinum
                Apr 8, 2019 at 7:12
Assuming you are using Spring boot.

Here are some things you can do to make it work (You might have done some of these, I added anything I can think of just to make sure):  
Remove your AppConfigUtil class because Spring boot will "magically" find the datasource for you if your application.properties is configured right.
Add @SpringBootApplication to your ConnerApplication.java class
Add spring-boot-starter-data-jpa dependency in your pom
Some side notes:

@Autowire is not intended to be marked with @Bean annotation. @Autowire CAN be used to autowire bean which is annotated with @Bean.
EDIT :

I realized that OP wants to deploy it on Glassfish. In that case, you will need to tweak Spring to produce a deployable war file and configure your application container (glassfish) to include a jdbc driver. All of it is doable but requires a lot of efforts.

I suggested that you go with embedded tomcat approach if you use Spring-boot for new project. It is basically battle-ready. You can hardly go wrong with this.
                Thanks for the advice Minjun.  I have taken your advice and "removed" (commented out the whole) appconfig file.  I then checked, and the class that runs the program is annotated with the following annotations: @SpringBootApplication @ComponentScan(basePackages={"com.connor"}) @EntityScan(basePackages={"com.connor.model"}) @EnableJpaRepositories(basePackages={"com.connor.dao"})  @EnableAutoConfiguration().  My pom.xml also contains the specified dependency.  I clean/install my project again, and still no luck.  Is there anything else I should look at?
– Connor Butch
                Jan 4, 2018 at 0:00
                If your SpringbootApplication class is at the root package which is com.conner (looks like it is from your picture), then only @SpringBootApplication is sufficient. This might not directly solve the problem though. Is there any new error message?
– Minjun Yu
                Jan 4, 2018 at 0:06
                I followed your suggestion and commented out all the annotations but the @SpringBootApplication one on my driver class.  However, I am still getting the same error.  Should I look at somehow including the mysql jar in the tomcat directory itself?
– Connor Butch
                Jan 4, 2018 at 0:12
                I re-read your question and realized you want to deploy the spring application on Glassfish. That means you will tweak Spring to produce a war file instead of "embedded-tomcat-jar" file. You also need to configure glassfish to include a jdbc driver so that when war file is deployed, it will find the jdbc-driver at runtime. All of this requires a lot of efforts, mind let me know why you want to use glassfish for spring while spring already provide a "standard-production-ready-embedded-tomcat" solution?
– Minjun Yu
                Jan 4, 2018 at 0:16
                Hi Minjun, I was unaware that spring tries to package my application for deployment on a tomcat server (I had assumed that I could choose whatever server I liked to deploy it, as I have done with regular jee apps in the past).  How should I configure my tomcat installation so that it has a mysql jdbc jar; should this be done in maven or via dropping the jar file in the tomcat installation directory?
– Connor Butch
                Jan 4, 2018 at 0:39
You don't need declare in pom.xml
spring.datasource.driver-class-name=com.mysql.jdbc.driver
You can read my configuration in a simple app using Spring Boot here
Beside, if you're using Spring Boot you don't need use codes "Source Code: the first relevant exception occurs when spring tries to inject the datasource bean that is a parameter to this method and can't create it..."
        
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