[SOLVED] Glassfish not importing mysql jdbc properly

I am trying to update my development environment from Eclipse Luna to Neon. I have cloned a Git repository of a jersey-quickstart-webapp and it is now deploying correctly.

However, when I try to access the application from the webpage, it throws the error below in the server console:

2017-04-01T14:43:57.528+0100|Warning: The following warnings have been detected: WARNING: Unknown HK2 failure detected:
MultiException stack 1 of 1 
javax.enterprise.inject.CreationException

Caused by: java.lang.Error: Unresolved compilation problems: 
The import com.mysql.jdbc.jdbc2 cannot be resolved
MysqlDataSource cannot be resolved to a type
The method unwrap(Class<MysqlDataSource>) from the type Wrapper refers to the missing type MysqlDataSource
MysqlDataSource cannot be resolved to a type
The method mysql_conn() from the type MySQL refers to the missing type MysqlDataSource

It seems to be complaining about the connection to the MySQL data source that I have already configured and have working in Eclipse Luna. The Glassfish server I am using is 4.1.1 (build 1) - the same as is working fine in Luna! Any ideas what is causing this error? All help much appreciated!

The full error trace is below:

2017-04-01T14:43:57.528+0100|Warning: The following warnings have been detected: WARNING: Unknown HK2 failure detected:
MultiException stack 1 of 1
javax.enterprise.inject.CreationException
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at java.lang.Class.newInstance(Class.java:442)
at org.jboss.weld.security.NewInstanceAction.run(NewInstanceAction.java:33)
at java.security.AccessController.doPrivileged(Native Method)
at org.jboss.weld.injection.Exceptions.rethrowException(Exceptions.java:40)
at org.jboss.weld.injection.Exceptions.rethrowException(Exceptions.java:50)
at org.jboss.weld.injection.Exceptions.rethrowException(Exceptions.java:90)
at org.jboss.weld.injection.ConstructorInjectionPoint.newInstance(ConstructorInjectionPoint.java:127)
at org.jboss.weld.injection.ConstructorInjectionPoint.invokeAroundConstructCallbacks(ConstructorInjectionPoint.java:92)
at org.jboss.weld.injection.ConstructorInjectionPoint.newInstance(ConstructorInjectionPoint.java:78)
at org.jboss.weld.injection.producer.AbstractInstantiator.newInstance(AbstractInstantiator.java:28)
at org.jboss.weld.injection.producer.BasicInjectionTarget.produce(BasicInjectionTarget.java:116)
at org.jboss.weld.injection.producer.BeanInjectionTarget.produce(BeanInjectionTarget.java:179)
at org.glassfish.jersey.ext.cdi1x.internal.AbstractCdiBeanHk2Factory$2.getInstance(AbstractCdiBeanHk2Factory.java:139)
at org.glassfish.jersey.ext.cdi1x.internal.AbstractCdiBeanHk2Factory._provide(AbstractCdiBeanHk2Factory.java:91)
at org.glassfish.jersey.ext.cdi1x.internal.GenericCdiBeanHk2Factory.provide(GenericCdiBeanHk2Factory.java:63)
at org.jvnet.hk2.internal.FactoryCreator.create(FactoryCreator.java:153)
at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:471)
at org.jvnet.hk2.internal.PerLookupContext.findOrCreate(PerLookupContext.java:70)
at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2072)
at org.jvnet.hk2.internal.ServiceLocatorImpl.internalGetService(ServiceLocatorImpl.java:767)
at org.jvnet.hk2.internal.ServiceLocatorImpl.getService(ServiceLocatorImpl.java:706)
at org.glassfish.jersey.internal.inject.Injections.getOrCreate(Injections.java:169)
at org.glassfish.jersey.server.model.MethodHandler$ClassBasedMethodHandler.getInstance(MethodHandler.java:284)
at org.glassfish.jersey.server.internal.routing.PushMethodHandlerRouter.apply(PushMethodHandlerRouter.java:74)
at org.glassfish.jersey.server.internal.routing.RoutingStage._apply(RoutingStage.java:109)
at org.glassfish.jersey.server.internal.routing.RoutingStage._apply(RoutingStage.java:112)
at org.glassfish.jersey.server.internal.routing.RoutingStage._apply(RoutingStage.java:112)
at org.glassfish.jersey.server.internal.routing.RoutingStage._apply(RoutingStage.java:112)
at org.glassfish.jersey.server.internal.routing.RoutingStage._apply(RoutingStage.java:112)
at org.glassfish.jersey.server.internal.routing.RoutingStage.apply(RoutingStage.java:92)
at org.glassfish.jersey.server.internal.routing.RoutingStage.apply(RoutingStage.java:61)
at org.glassfish.jersey.process.internal.Stages.process(Stages.java:197)
at org.glassfish.jersey.server.ServerRuntime$2.run(ServerRuntime.java:301)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:317)
at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:292)
at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1139)
at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:460)
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:386)
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:334)
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:221)
at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1682)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:318)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:160)
at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:734)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:673)
at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:174)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:416)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:283)
at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:459)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:167)
at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:206)
at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:180)
at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:235)
at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:283)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:200)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:132)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:111)
at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:536)
at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:112)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:117)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:56)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:137)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:591)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:571)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.Error: Unresolved compilation problems: 
The import com.mysql.jdbc.jdbc2 cannot be resolved
MysqlDataSource cannot be resolved to a type
MysqlDataSource cannot be resolved to a type
MysqlDataSource cannot be resolved to a type
MysqlDataSource cannot be resolved to a type
MysqlDataSource cannot be resolved to a type
The method unwrap(Class<MysqlDataSource>) from the type Wrapper refers to the missing type MysqlDataSource
MysqlDataSource cannot be resolved to a type
MysqlDataSource cannot be resolved to a type
MysqlDataSource cannot be resolved to a type
The method mysql_conn() from the type MySQL refers to the missing type MysqlDataSource
at com.pododdle.dao.MySQL.<init>(MySQL.java:11)
at com.pododdle.dao.UserService.<init>(UserService.java:14)
at com.pododdle.resources.UserResource.<init>(UserResource.java:23)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at org.jboss.weld.injection.ConstructorInjectionPoint.newInstance(ConstructorInjectionPoint.java:119)
... 66 more

2017-04-01T14:43:57.529+0100|Warning: StandardWrapperValve[Jersey Web Application]: Servlet.service() for servlet Jersey Web Application threw exception
java.lang.Error: Unresolved compilation problems: 
The import com.mysql.jdbc.jdbc2 cannot be resolved
MysqlDataSource cannot be resolved to a type
MysqlDataSource cannot be resolved to a type
MysqlDataSource cannot be resolved to a type
MysqlDataSource cannot be resolved to a type
MysqlDataSource cannot be resolved to a type
The method unwrap(Class<MysqlDataSource>) from the type Wrapper refers to the missing type MysqlDataSource
MysqlDataSource cannot be resolved to a type
MysqlDataSource cannot be resolved to a type
MysqlDataSource cannot be resolved to a type
The method mysql_conn() from the type MySQL refers to the missing type MysqlDataSource
at com.pododdle.dao.MySQL.<init>(MySQL.java:11)
at com.pododdle.dao.UserService.<init>(UserService.java:14)
at com.pododdle.resources.UserResource.<init>(UserResource.java:23)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at org.jboss.weld.injection.ConstructorInjectionPoint.newInstance(ConstructorInjectionPoint.java:119)
at org.jboss.weld.injection.ConstructorInjectionPoint.invokeAroundConstructCallbacks(ConstructorInjectionPoint.java:92)
at org.jboss.weld.injection.ConstructorInjectionPoint.newInstance(ConstructorInjectionPoint.java:78)
at org.jboss.weld.injection.producer.AbstractInstantiator.newInstance(AbstractInstantiator.java:28)
at org.jboss.weld.injection.producer.BasicInjectionTarget.produce(BasicInjectionTarget.java:116)
at org.jboss.weld.injection.producer.BeanInjectionTarget.produce(BeanInjectionTarget.java:179)
at org.glassfish.jersey.ext.cdi1x.internal.AbstractCdiBeanHk2Factory$2.getInstance(AbstractCdiBeanHk2Factory.java:139)
at org.glassfish.jersey.ext.cdi1x.internal.AbstractCdiBeanHk2Factory._provide(AbstractCdiBeanHk2Factory.java:91)
at org.glassfish.jersey.ext.cdi1x.internal.GenericCdiBeanHk2Factory.provide(GenericCdiBeanHk2Factory.java:63)
at org.jvnet.hk2.internal.FactoryCreator.create(FactoryCreator.java:153)
at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:471)
at org.jvnet.hk2.internal.PerLookupContext.findOrCreate(PerLookupContext.java:70)
at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2072)
at org.jvnet.hk2.internal.ServiceLocatorImpl.internalGetService(ServiceLocatorImpl.java:767)
at org.jvnet.hk2.internal.ServiceLocatorImpl.getService(ServiceLocatorImpl.java:706)
at org.glassfish.jersey.internal.inject.Injections.getOrCreate(Injections.java:169)
at org.glassfish.jersey.server.model.MethodHandler$ClassBasedMethodHandler.getInstance(MethodHandler.java:284)
at org.glassfish.jersey.server.internal.routing.PushMethodHandlerRouter.apply(PushMethodHandlerRouter.java:74)
at org.glassfish.jersey.server.internal.routing.RoutingStage._apply(RoutingStage.java:109)
at org.glassfish.jersey.server.internal.routing.RoutingStage._apply(RoutingStage.java:112)
at org.glassfish.jersey.server.internal.routing.RoutingStage._apply(RoutingStage.java:112)
at org.glassfish.jersey.server.internal.routing.RoutingStage._apply(RoutingStage.java:112)
at org.glassfish.jersey.server.internal.routing.RoutingStage._apply(RoutingStage.java:112)
at org.glassfish.jersey.server.internal.routing.RoutingStage.apply(RoutingStage.java:92)
at org.glassfish.jersey.server.internal.routing.RoutingStage.apply(RoutingStage.java:61)
at org.glassfish.jersey.process.internal.Stages.process(Stages.java:197)
at org.glassfish.jersey.server.ServerRuntime$2.run(ServerRuntime.java:301)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:317)
at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:292)
at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1139)
at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:460)
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:386)
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:334)
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:221)
at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1682)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:318)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:160)
at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:734)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:673)
at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:174)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:416)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:283)
at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:459)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:167)
at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:206)
at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:180)
at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:235)
at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:283)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:200)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:132)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:111)
at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:536)
at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:112)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:117)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:56)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:137)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:591)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:571)
at java.lang.Thread.run(Thread.java:745)

EDIT 1: As the comment of Mark Rotteveel suggested that I am missing the MySQL Connector J from my classpath, I am now including the Maven dependency I have for the connector in my pom.xml. I would have thought that this was sufficient - do I need to include the jar for the MySQL Connector/J in the Glassfish classpath aswell?

    <!-- MySQL Connector/J -->
    <dependency>
        <groupId>mysql</groupId>
        <artifactId>mysql-connector-java</artifactId>
        <version>6.0.6</version>
    </dependency>

EDIT 2: As per Deltharis's comment, I placed the mysql-connector-java-6.0.6.jar in the glassfish lib directory. This, however, has made no difference to the error message.