Lets take scenario #3 first.
I think your local mysql server have reached its value of max connection. You can check the value of max connection of your mysql server with this query:
mysql> select @@global.max_connections;
If you find this value low, then you can change it to a large value with this query::
mysql>set @@global.max_connections = 1000;
That might solve your MySQLNonTransientConnectionException.
Now to your scenario #2. Have you try and run your select query to cloud-sql web interface? Is it selecting your table there? If the query is working there then there is no problem with the query. Try to eliminate PreparedStatement object like :: ResultSet rs = c.createStatement().executeQuery("your query string here");
---Abhishek
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