Backstory, I would like to build shiny apps to give to some of our data collectors so they can review what has been collected. We currently house all of our data in a cloud based MySQL server. Ideally, I would like the shiny app to pull data directly from the MySQL server so it can be fully automated without any data pulls and up 24/7.
I have been trying to first just build the connection between R and MySQL using the RMySQL package and can't seem to get it working. I have set up a specific username/password for this connection that is read only(however I have also tried my regular username which has all privileges granted). This is the code I am running;
mydb=dbConnect(
MySQL(),
user='myuser',
password='mypass',
dbname='vgtg',
host='ipaddress',
port=3306,
)
Obviously the 'ipaddress' of the server has been changed for the sake of posting here but it is a generic looking address like
'192.168.1.1'
When I run the code above I get this error message;
Error in .local(drv, ...) :
Failed to connect to database: Error: Can't connect to MySQL server on
'ipaddress' (0)
I have tried looking for previous questions posted but none seem to be exactly this error message that I am receiving. It makes me think that for some reason RMySQL is looking locally for the server when it is actually a cloud based, remote, server.
Also, is there anything more I should set up server side to allow the connection? I do have a server admin to help out but I am not sure how familiar he is with R and likewise I am not particularly familiar with working with servers. He has opened port 3306 for me and is able to see my attempts to connect through the port.
Your syntax is correct with the exception of
port=3306,
You need to drop the comma. That said, the error you received is unrelated to the syntax.
Without knowing the details of your setup, it is hard to diagnose. Where does the MySQL DB reside? For example, if it is on an AWS RDS instance, then the host isn't a standard IP address, it is something like this
mydb.cm1abc2v4mod.us-west-1.rds.amazonaws.com
Assuming that the IP address you used is correct, then the problem is most likely on the server. You need to ensure that port 3306 is open to traffic. Otherwise, R will not be able to connect to the DB.
Related
I am using the following DBD::mysql statement to connect to a MySQL database:
use DBI;
# Connect to the database.
my $dbh = DBI->connect("DBI:mysql:database=test;host=localhost",
"usr", "usr's password",
{'RaiseError' => 1});
Is there a way to check if MySQL service is running, before trying to connect to the database? What if the database is running on a remote server?
If you want a solution to check if the service is running without attempting to connect to it, you could use some Perl package to check the process table (works locally only), or check that the MySQL port (3306 by default) has a process listening to it.
I'm not sure what the purpose of this check is, because even if the service is running, the next thing you'll probably want to do is open a DB connection. Opening a DB connection is a quick and easy thing to do, and it has good error reporting if it doesn't work. So your intention to check that the service is running first is just unnecessary overhead.
I would just try to connect as you are doing. This is the most direct way of checking that the service is running, and it works both locally and remotely.
If there's an error, catch the error and interpret the error message. It'll be error 2002 (for localhost) or 2003 (for TCP/IP, whether it's the same host or a remote host).
These errors are mostly reliable. But there could be red herrings, for example if the service is running on a remote host, but your client host can't reach it because of firewalls or routing issues.
If you get an error 1045 (Access Denied), at least you know the service is running and you can reach it, the problem is only that your user & password are incorrect, or you tried to access a schema you don't have privilege to use.
I am trying to run this command locuscompare(in_fn1 = gwas_fn, in_fn2 = eqtl_fn, title1 = 'CAD GWAS', title2 = 'Coronary Artery eQTL') within R in ubuntu behind a corporate proxy
but having the following persistent issue for three days.
Error in .local(drv, ...) :
Failed to connect to database: Error: Can't connect to MySQL server on 'locuscompare-us-west-2a.xxxxxx.us-west-2.rds.amazonaws.com' (111)
Warning message:
In rm(config) : object 'config' not found
I have already tried the solutions mentioned in stack overflow, such as installing MySQL, assigning users' privilege, editing bind-address in configuration file, but still do not know how to run it smoothly.
I thought at first it was an issue related to the lacking of MySQL server and AWS account on my device. But, when I use it on my mac with home Wi-Fi, it is working like a charm without any installation and creation of MySQL server and AWS account. However, I still need to use this tool on my work PC because of input data privacy issue.
Does it mean I need to create an AWS account and adjust the network setting in it to access MySQL server on this URL 'locuscompare-us-west-2a.xxxxx.us-west-2.rds.amazonaws.com'? (Sorry that I am very new to AWS and MySQL.)
Please let me know how to run this tool behind a corporate proxy.
I have bought a basic 6$ pythonanywhere server which allows for SCP and SSH connections to their servers. I have deployed my flask application (REST API) to the server and set up a local environment (installed packages, set up path and environmental variables). I ran the app, and it gives me the 404 page on the / route which is actually a sign that it is working.
However when I try to hit a route like /api/users/3 for example, it gives me an error 500 (internal server error). I dug around some log files on the server and found one which is basically the output of the WSGI web server which is host to my flask application. It said that there is an issue with the database communication. From what I understand, it connected successfully but it couldn't query the data from the table:
(1044, "Access denied for user 'secret_username'#'%' to database 'test'")
I have tried to fix this through the web mysql console by giving my <secret_username>#secret_username.pythonanywhere.com all the privilages to test.*, but it gives me an access error once again. I tried to SSH into the machine that is host to the mysql server and tried to connect to it - secret_username.mysql.pythonanywhere-services.com but it doesn't allow me to ssh into this server.
Has anyone experienced this issue? I am almost sure that my connection is set up correctly because if it didn't establish connection it would give me an access error with message `using password "yes". I've read on forums a bit, they suggest installing a mysql server on the same server as the flask application, but I don't have access to sude for some reason, probably due to my cheap plan. Any ideas?
If you are using the MySQL database provided by PythonAnywhere, with the hostname secret_username.mysql.pythonanywhere-services.com, then your database will be called secret_username$test, not just test -- see the "Databases" page on the PythonAnywhere website.
I'm using Outsystems Service Studio to develop a web application. I need to configure a connection to access a local server database. I get "Connection String test failed: Unable to connect to any of the specified MySQL hosts." I just figured out I can't connect using "localhost", because the Outsystems server is not local, but I'm not able to find a solution. what is wrong? Other details:
MySQL Server is up and running
I selected MySQL in DBMS
Inserted my schema name
Inserted the username (with all privileges granted)
Inserted the user password
Tried both basic and advanced configuration. I inserted j"dbc:mysql://127.0.0.1:3306/mydb?user=outsystems2" as connection string parameters and I get "Connection String test failed: Keyword not supported.Parameter name: mysql://127.0.0.1:3306/mydb?user". I know this connection string can't work , but I'm not able to find a functioning one. I've read many guides about this configuration, but no solution was found. Thank you all for your time and help, feel free to ask for more details
Luciano,
Is your OutSystems environment on-premises or in the cloud? Either way, you need to make sure that this server is able to reach - it as connectivity - to your MySQL database server. Using localhost or 127.0.0.1 is pretty much the same thing as this is an address for the machine where the request is running, which is, in this case, the OutSystems server. Do you have the MySQL database on your local machine? This is not a good approach as you will need to have an address that won't change otherwise the connection won't be stable and you'd have to reconfigure it all the time.
Regards
I am continuously getting below error while connecting to mysql-
Can\'t connect to MySQL server on /ip/address
but mysql is not generating any log for this error. I have below entries in my.cnf file
log=/var/log/mysql_err.log
log-error=/var/log/mysql/mysql_error.log
I am using correct credentials. No issue of conections.
Now how will I determine the exact issue If I'll not get any log ?
Any Idea, how to solve this ?
This is not surprising:
the server can only log an incident it is aware of. However your client does not even reach the server at all! So how should the server know some client has attempted to contact it?
The error message you get clearly indicates that you do have a connection issue.
You can easily make a test to check the most common problems: just open a telnet connection from the system trying to connect to the system the sql server runs on, connect to the mysql port: telnet <ip-of-mysql-server> mysql
On typical unixoid systems "mysql" will be substituted by the "well known port number of mysql, which is 3306. otherwise you have to specify it manually. Do you get a connection at all? I would guess not. This means either the mysql server is not listening where expected (not running or configured otherwise) or the connection is blocked on network level (firewall).