[SOLVED] PersistenceManager cannot connect to database

When trying to run app which uses Jackrabbit (locally on Tomcat7), from any reason it doesn't connect to database. Connection to db works from regular Java app with the same credentials. How to investigate what is wrong about connectivity? There is a question Cannot instantiate persistence manager org.apache.jackrabbit.core.persistence.pool.MySqlPersistenceManager but no explanation.

DB connection configuration:

<PersistenceManager class="org.apache.jackrabbit.core.persistence.pool.MySqlPersistenceManager">
      <param name="driver" value="com.mysql.jdbc.Driver"/>
      <param name="url" value="jdbc:mysql://localhost:3306/repo"/>
      <param name="databaseType" value="mysql"/>
      <param name="user" value="admin" />
      <param name="password" value="password11.." />
      <param name="schemaObjectPrefix" value="${wsp.name}_"/>
      <param name="externalBLOBs" value="true"/>
</PersistenceManager>

Error output:

[localhost-startStop-1] INFO org.apache.jackrabbit.core.RepositoryImpl - Starting repository...
[localhost-startStop-1] INFO org.apache.jackrabbit.core.fs.local.LocalFileSystem - LocalFileSystem initialized at path jackrabbit\repository
[localhost-startStop-1] INFO org.apache.jackrabbit.core.fs.local.LocalFileSystem - LocalFileSystem initialized at path jackrabbit\version
Tue Aug 21 10:46:47 CEST 2018 WARN: Establishing SSL connection without server's identity verification is not recommended. According to MySQL 5.5.45+, 5.6.26+ and 5.7.6+ requirements SSL connection must be established by default if explicit option isn't set. For compliance with existing applications not using SSL the verifyServerCertificate property is set to 'false'. You need either to explicitly disable SSL by setting useSSL=false, or set useSSL=true and provide truststore for server certificate verification.
[localhost-startStop-1] ERROR org.apache.jackrabbit.core.RepositoryImpl - failed to start Repository: Cannot instantiate persistence manager org.apache.jackrabbit.core.persistence.pool.MySqlPersistenceManager
javax.jcr.RepositoryException: Cannot instantiate persistence manager org.apache.jackrabbit.core.persistence.pool.MySqlPersistenceManager
    at org.apache.jackrabbit.core.RepositoryImpl.createPersistenceManager(RepositoryImpl.java:1379)
    at org.apache.jackrabbit.core.RepositoryImpl.createVersionManager(RepositoryImpl.java:512)
    at org.apache.jackrabbit.core.RepositoryImpl.<init>(RepositoryImpl.java:313)
    at org.apache.jackrabbit.core.RepositoryImpl.create(RepositoryImpl.java:615)
    at org.apache.jackrabbit.core.TransientRepository$3.getRepository(TransientRepository.java:250)
    at org.apache.jackrabbit.core.TransientRepository.startRepository(TransientRepository.java:280)
    at org.apache.jackrabbit.core.TransientRepository.login(TransientRepository.java:376)
    at org.apache.jackrabbit.commons.AbstractRepository.login(AbstractRepository.java:144)
    at org.omilab.services.repo.service.JackRabbitRepositoryProvider.<init>(JackRabbitRepositoryProvider.java:60)
    at org.omilab.services.repo.service.JackRabbitRepositoryProvider.getInstance(JackRabbitRepositoryProvider.java:41)
    at org.omilab.services.repo.service.JackRabbitConnector.<init>(JackRabbitConnector.java:45)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
    at java.lang.reflect.Constructor.newInstance(Unknown Source)
    at java.lang.Class.newInstance(Unknown Source)
    at codes.thischwa.c5c.ConnectorServlet.init(ConnectorServlet.java:79)
    at javax.servlet.GenericServlet.init(GenericServlet.java:158)
    at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1282)
    at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1195)
    at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1085)
    at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:5318)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5610)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1092)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1984)
    at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
Caused by: org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (Could not create connection to database server.)
    at org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1549)
    at org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1388)
    at org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044)
    at org.apache.jackrabbit.core.util.db.ConnectionHelper.getExtraNameCharacters(ConnectionHelper.java:187)
    at org.apache.jackrabbit.core.util.db.ConnectionHelper.prepareDbIdentifier(ConnectionHelper.java:142)
    at org.apache.jackrabbit.core.persistence.pool.BundleDbPersistenceManager.init(BundleDbPersistenceManager.java:542)
    at org.apache.jackrabbit.core.persistence.pool.MySqlPersistenceManager.init(MySqlPersistenceManager.java:51)
    at org.apache.jackrabbit.core.RepositoryImpl.createPersistenceManager(RepositoryImpl.java:1375)
    ... 33 more

EDIT1:

on the same tomcat built with the same maven this simple app can connect to the same database:

<%@ page import="java.sql.*"%>
<html>
<head>
<title>DB</title>
</head>
<body>
    <h1>DB connectivity test!</h1>

        <%
  String db = "repo";
  String user = "admin"; 
  String password = "password11..";
  try {
    java.sql.Connection con;
    Class.forName("org.gjt.mm.mysql.Driver");
    con = DriverManager.getConnection("jdbc:mysql://localhost/"+db, user, password);
    out.println (db+ " database successfully opened.");
  }
  catch(SQLException e) {
    out.println("SQLException caught: " +e.getMessage());
  }
%>


</body>