Not Able to connect wso2 with mysql?

Question

I am using WSO2 IS 5.9.0 all the setting are proper accoriding to this documentation https://is.docs.wso2.com/en/5.9.0/setup/changing-to-mysql/ and facing the following problem related to MySQL JDBC Driver and also tried many solution but i am still stuck.

[2019-11-29 11:27:37,591] [] ERROR {org.wso2.carbon.identity.scim2.common.utils.AdminAttributeUtil} - Error occurred while updating the admin groups's attributes in Tenant ID : -1234, Error : 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. org.wso2.carbon.identity.base.IdentityRuntimeException: 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 org.wso2.carbon.identity.base.IdentityRuntimeException.error(IdentityRuntimeException.java:71)
    at org.wso2.carbon.identity.core.persistence.JDBCPersistenceManager.getDBConnection(JDBCPersistenceManager.java:163)
    at org.wso2.carbon.identity.core.util.IdentityDatabaseUtil.getDBConnection(IdentityDatabaseUtil.java:54)
    at org.wso2.carbon.identity.core.util.IdentityDatabaseUtil.getDBConnection(IdentityDatabaseUtil.java:43)
    at org.wso2.carbon.identity.scim2.common.DAO.GroupDAO.isExistingGroup(GroupDAO.java:84)
    at org.wso2.carbon.identity.scim2.common.DAO.GroupDAO.addSCIMGroupAttributes(GroupDAO.java:143)
    at org.wso2.carbon.identity.scim2.common.group.SCIMGroupHandler.addMandatoryAttributes(SCIMGroupHandler.java:76)
    at org.wso2.carbon.identity.scim2.common.utils.AdminAttributeUtil.updateAdminGroup(AdminAttributeUtil.java:136)
    at org.wso2.carbon.identity.scim2.common.internal.SCIMCommonComponent.activate(SCIMCommonComponent.java:96)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.eclipse.equinox.internal.ds.model.ServiceComponent.activate(ServiceComponent.java:260)
    at org.eclipse.equinox.internal.ds.model.ServiceComponentProp.activate(ServiceComponentProp.java:146)
    at org.eclipse.equinox.internal.ds.model.ServiceComponentProp.build(ServiceComponentProp.java:345)
    at org.eclipse.equinox.internal.ds.InstanceProcess.buildComponent(InstanceProcess.java:620)
    at org.eclipse.equinox.internal.ds.InstanceProcess.buildComponents(InstanceProcess.java:197)
    at org.eclipse.equinox.internal.ds.Resolver.getEligible(Resolver.java:343)
    at org.eclipse.equinox.internal.ds.SCRManager.serviceChanged(SCRManager.java:222)
    at org.eclipse.osgi.internal.serviceregistry.FilteredServiceListener.serviceChanged(FilteredServiceListener.java:113)
    at org.eclipse.osgi.internal.framework.BundleContextImpl.dispatchEvent(BundleContextImpl.java:985)
    at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:234)
    at org.eclipse.osgi.framework.eventmgr.ListenerQueue.dispatchEventSynchronous(ListenerQueue.java:151)
    at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.publishServiceEventPrivileged(ServiceRegistry.java:866)
    at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.publishServiceEvent(ServiceRegistry.java:804)
    at org.eclipse.osgi.internal.serviceregistry.ServiceRegistrationImpl.register(ServiceRegistrationImpl.java:130)
    at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.registerService(ServiceRegistry.java:228)
    at org.eclipse.osgi.internal.framework.BundleContextImpl.registerService(BundleContextImpl.java:525)
    at org.eclipse.osgi.internal.framework.BundleContextImpl.registerService(BundleContextImpl.java:544)
    at org.eclipse.osgi.internal.framework.BundleContextImpl.registerService(BundleContextImpl.java:1071)
    at org.wso2.carbon.user.mgt.internal.UserMgtDSComponent.activate(UserMgtDSComponent.java:172)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.eclipse.equinox.internal.ds.model.ServiceComponent.activate(ServiceComponent.java:260)
    at org.eclipse.equinox.internal.ds.model.ServiceComponentProp.activate(ServiceComponentProp.java:146)
    at org.eclipse.equinox.internal.ds.model.ServiceComponentProp.build(ServiceComponentProp.java:345)
    at org.eclipse.equinox.internal.ds.InstanceProcess.buildComponent(InstanceProcess.java:620)
    at org.eclipse.equinox.internal.ds.InstanceProcess.buildComponents(InstanceProcess.java:197)
    at org.eclipse.equinox.internal.ds.Resolver.getEligible(Resolver.java:343)
    at org.eclipse.equinox.internal.ds.SCRManager.serviceChanged(SCRManager.java:222)
    at org.eclipse.osgi.internal.serviceregistry.FilteredServiceListener.serviceChanged(FilteredServiceListener.java:113)
    at org.eclipse.osgi.internal.framework.BundleContextImpl.dispatchEvent(BundleContextImpl.java:985)
    at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:234)
    at org.eclipse.osgi.framework.eventmgr.ListenerQueue.dispatchEventSynchronous(ListenerQueue.java:151)
    at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.publishServiceEventPrivileged(ServiceRegistry.java:866)
    at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.publishServiceEvent(ServiceRegistry.java:804)
    at org.eclipse.osgi.internal.serviceregistry.ServiceRegistrationImpl.register(ServiceRegistrationImpl.java:130)
    at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.registerService(ServiceRegistry.java:228)
    at org.eclipse.osgi.internal.framework.BundleContextImpl.registerService(BundleContextImpl.java:525)
    at org.eclipse.osgi.internal.framework.BundleContextImpl.registerService(BundleContextImpl.java:544)
    at org.wso2.carbon.identity.core.internal.IdentityCoreServiceComponent.activate(IdentityCoreServiceComponent.java:171)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.eclipse.equinox.internal.ds.model.ServiceComponent.activate(ServiceComponent.java:260)
    at org.eclipse.equinox.internal.ds.model.ServiceComponentProp.activate(ServiceComponentProp.java:146)
    at org.eclipse.equinox.internal.ds.model.ServiceComponentProp.build(ServiceComponentProp.java:345)
    at org.eclipse.equinox.internal.ds.InstanceProcess.buildComponent(InstanceProcess.java:620)
    at org.eclipse.equinox.internal.ds.InstanceProcess.buildComponents(InstanceProcess.java:197)
    at org.eclipse.equinox.internal.ds.Resolver.getEligible(Resolver.java:343)
    at org.eclipse.equinox.internal.ds.SCRManager.serviceChanged(SCRManager.java:222)
    at org.eclipse.osgi.internal.serviceregistry.FilteredServiceListener.serviceChanged(FilteredServiceListener.java:113)
    at org.eclipse.osgi.internal.framework.BundleContextImpl.dispatchEvent(BundleContextImpl.java:985)
    at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:234)
    at org.eclipse.osgi.framework.eventmgr.ListenerQueue.dispatchEventSynchronous(ListenerQueue.java:151)
    at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.publishServiceEventPrivileged(ServiceRegistry.java:866)
    at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.publishServiceEvent(ServiceRegistry.java:804)
    at org.eclipse.osgi.internal.serviceregistry.ServiceRegistrationImpl.register(ServiceRegistrationImpl.java:130)
    at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.registerService(ServiceRegistry.java:228)
    at org.eclipse.osgi.internal.framework.BundleContextImpl.registerService(BundleContextImpl.java:525)
    at org.eclipse.osgi.internal.framework.BundleContextImpl.registerService(BundleContextImpl.java:544)
    at org.wso2.carbon.core.init.CarbonServerManager.initializeCarbon(CarbonServerManager.java:529)
    at org.wso2.carbon.core.init.CarbonServerManager.removePendingItem(CarbonServerManager.java:305)
    at org.wso2.carbon.core.init.PreAxis2ConfigItemListener.bundleChanged(PreAxis2ConfigItemListener.java:118)
    at org.eclipse.osgi.internal.framework.BundleContextImpl.dispatchEvent(BundleContextImpl.java:973)
    at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:234)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:345)
Caused by: com.mysql.cj.jdbc.exceptions.CommunicationsException: Communications link failure

Answer 1

Looks like a similar issue was already reported and tracked with this git issue. Refer the git issue and as a workaround Disabling SSL through the connection url in master-datasource.xml worked will work

You can try by

[database.shared_db]
type = "mysql"
url= "jdbc:mysql://127.0.0.1:3306/regdb?useSSL=false"
username = "wso2is"
password="wso2is"

If you give url as a key, then no need to give hostname,port and dbname separately.