I'm trying to create shiny app in shiny.io which requires access to a MySQL database which is located in my local machine. Is it possible to use RMySQL to connect to the local database by shiny.io? And how can I do that?
I'm a little "late" with my answer, but keep in mind that if you are deploying to shiny.io then "localhost" is pointing to shiny.io and there is no mysql for you there :-) So you should have to open your MySQL server and use your public IP address in "host" variable. Not that I am proposing this, from the security point of view it is not wise to open your MySQL server to the public. If you follow this way, at least, you should filter connections to only allow the IP address of shiny.io.
Another solution -more reasonable, in my opinion- might be to use an already public server that offers you a persistence layer, such as mongohq.com (now compose.io). They use MongoDB (not MySQL) but it could satisfy your needs (and you will get a 512MB RAM testing server for free). You may want to study this working example that uses shiny.io and mongo in order to start your project up.
The usage is essentially the same as in regular R script.
you can put this at the top of your server.R file
library(RMySQL)
con = dbConnect(MySQL(), user='myusername', password='mysillypassword', db='dataaa', host='localhost')
query = "SELECT 1"
result = dbGetQuery(con, query)
Now result will be available for the rest of the shiny app.
You can also build the query inside a reactive function, and dynamically query the database.
Within your mySQL database, whitelist shinyapps.io IP addresses.
See this helpful post from Rstudio support.
Related
I'm writing some R code that queries a MongoDB database, imports records matching the query criteria into R, performs record linkage with another data source, and then pushes the updated records back into MongoDB.
The code needs to work with any instance of the MongoDB database. Some people have it installed as standalone on their own computers, while others have it installed on their organisational servers. Note that these are servers specific to individual organisations and not the public mongo server.
To test my code, I have access to both scenarios - one instance is set up on my own computer, and I have several remote server instances as well.
The MongoDB database has some APIs, but I was struggling with the adapting the APIs to include the correct syntax to form my query, so I thought I would try the mongolite package instead.
I was able to create a successful connection string for the MongoDB instance on my local computer, using my user ID (which I retrieve first with an API and save as the R object myids), password, the localhost and port number as below:
# Load library:
library(mongolite)
# Create connection:
con <- mongolite::mongo(collection = "person",
db = "go-data",
url = paste0("mongodb://localhost:3000",
myids$userid,
":",
rawToChar(password)))
I understood from reading the mongolite user manual that to create the connection string / URI, you skip the http or https part of the address and preface it with either mongodb:// when the Mongodb database is on a local computer, or mongodb+srv:// when the Mongodb database is on a remote server.
However, when I try just changing the prefix and login details for the remote server version, the connection fails. Say the URL for my remote server is https://mydb-r21.orgname.org/ which opens a web page where you can log in to the Mongodb database and interact with it via a graphical user interface. Just swapping localhost:3000 for the web address mydb-r21.orgname.org/ and supplying the relevant login credentials for that server doesn't work:
# Load library:
library(mongolite)
# Create connection:
con <- mongolite::mongo(collection = "person",
db = "go-data",
url = paste0("mongodb+srv://mydb-r21.orgname.org/",
myids$userid,
":",
rawToChar(password)))
When I try, this is the error I get:
Warning: [ERROR] Failed to look up SRV record "_mongodb._tcp.mydb-r21.orgname.org": DNS name does not exist.
Error: Invalid uri_string. Try mongodb://localhost
If I try changing to mongodb::// (not localhost because it isn't hosted locally) I get this:
Error: No suitable servers found (`serverSelectionTryOnce` set): [connection timeout calling hello on 'mydb-r21.orgname.org:27017']
Interestingly, the port that is suffixed in the error message is the correct one that I was expecting, but that still doesn't help me.
The documentation in the mongolite user manual and other places I've found online seem to add some read/write specifications to the connection string, but as I'm not very familiar with how connection strings are constructed, I don't know if these are specific to the databases they are using in their examples. I can't find any clear explanation of what the extra bits that are not part of the URL mean, e.g. as shown in this blog. All the prefixes seem to be a bit different too, so I am not even sure what would be appropriate to try in my case.
Can anyone explain why the connection string works fine with localhost:port number for the local instance, but doesn't work with the URL for the remote server / online instance?
Also what do I need to do to make the URI for the remote server valid?
I have been working on SQL Server 2017 via R (on Rstudio as well as R on SSMS) and i am unable to connect to a specific database. I mention the database name in the connection prompt but, it gets connected only to the master database. Is there something that I am missing while connecting?
The syntax I use for connection is:
conn = "Driver={ODBC Driver 13 for SQL Server};server=;Uid=uid; pwd=pwd;Database = mydb"
I am trying to use both RevoscaleR as well as ODBC() package in Rstudio to connect to a specific database but, it still gets connected to master database. Using RStudio connections pane, if i try to explore the other databases, it shows only dbo schemas and no other schemas even if they exist. Can someone help me in figuring out what might have gone wrong?
Most likely the login you use (the uid) is not authorized for that particular database (it is not created as a user in that database).
Some example code you can run in SSMS as - for example - sa:
--switch over to the database in question
USE mydb
GO
CREATE USER uid FOR LOGIN uid;
The above code creates a user in the database in question with the same name as the login.
Hope this helps!
Apparently, using AttachDbFilename and user instance in your connection string is a bad way to connect to a DB. I'm using SQL server express on my local machine and it all seems to work fine. But what's the proper way to connect to SQL server then?
Thanks for your explanation.
Using User Instance means that SQL Server is creating a special copy of that database file for use by your program. If you have two different programs using that same connection string, they get two entirely different copies of the database. This leads to a lot of confusion, as people will test updating data with their program, then connect to a different copy of their database in Management Studio, and complain that their update isn't working. This sends them through a flawed series of wild goose chase steps trying to troubleshoot the wrong problem.
This article goes into more depth about how to use this feature, but heed the very first note: the User Instance feature has been deprecated. In SQL Server 2012, the preferred alternatives are (in this order, IMHO):
Create or attach your database to a real instance of SQL Server. Your connection string will then just need to specify the instance name, the database name, and credentials. There will be no mixup as Management Studio, Visual Studio and your program(s) will all be connecting to a single copy of the database.
Use a container for local development. Here's a great starter video by Anna Hoffman and Anthony Nocentino, and I have some other resources here, here, and here. If you're on an M1 Mac, you won't be able to use a full-blown SQL Server instance, but you can use Azure SQL Edge if you can get by with most SQL Server functionality (the omissions are enumerated here).
Use SqlLocalDb for local development. I believe I pointed you to this article yesterday: "Getting Started with SQL Server 2012 Express LocalDB."
Use SQL Server Compact. I like this option the least because the functionality and syntax is not the same - so it's not necessarily going to provide you with all the functionality you're ultimately going to want to deploy. Compact Edition is also deprecated, so there's that.
Of course if you are using a version < SQL Server 2012, SqlLocalDb is not an option - so you should be creating a real database and using that consistently. I only mention the Compact option for completeness - I think that can be almost as bad an idea as using AttachDbFileName.
EDIT: I've blogged about this here:
Bad Habits : Using AttachDBFileName
In case someone had the problem.
When attaching the database with a connection string containing AttachDBFile
with SQLEXPRESS, I noticed this connection was exclusive to the ASP.NET application that was using the database. The connection did block the access to all other processes on the file level when made with System.Data.SqlClient as provider.
In order to assure the connection to be shareable with other processes
instead use DataBase to specify the database name in your connection string
Example or connection string :
Data Source=.\SQLEXPRESS;DataBase=PlaCliGen;User ID=XXX;password=ZZZ; Connect Timeout=30
,where PlaCliGen is the name (or logical name) by which SQLEXPRESS server knows the database.
By connecting to the data base with AttachDBFile giving the path to the .mdf file
(namely : replacing DataBase = PlacliGen by AttachDBFile = c:\vs\placligen\app_data\placligen.mdf) the File was connected exclusively and no other process could connect to the database.
I kind of new to SQL Server, I always used access db for my sites.
I created a SQL Server on my local computer and now I want to take this db and transfer it to the server. In access all I had to do is, take the mdb file and put it on the server and change the connection string. How can I transfer the SQL Server db to the server?
Is there any file to put on the server ?
Also the connection string isn't a folder but a local computer like this:
Data Source=my-PC;Initial Catalog=storeSQL1;User ID='my-PC\com';Password='';Trusted_Connection=YES;
Who can provide me this connection string for the server (the hosting company) ?
The easiest way would probably be to create a backup of the database on your local machine, then restore that backup on the new server.
Roadmap is:
Do simple backup-restore to move user databases to target server.
Create script on source server, that can recover permissions and login-users pairing
Restore the CLR and TRUSTWORTHY security for databases, that using unsafe assemblies, simpliest way is (in proper DB):
exec sp_changedbowner 'sa' --sa just for example
ALTER DATABASE dbname SET TRUSTWORTHY ON
Enjoy
Depending on your version of SQL Server here is a good article that outlines all the ways to move a SQL Server Database.
http://blogs.msdn.com/b/sreekarm/archive/2009/09/11/move-a-database-from-one-server-to-another-server-in-sql-server-2008.aspx
As for getting the connection string yes the hosting company would provide you with that. Where is the database hosted, you could check their knowledge base articles or if it's an in house data base I'm sure a dba could provide you with that information. It won't change much from what you have but it will change.
I'm not sure what tools your using, but to start you need to do a dump or backup of your current database on your machine. After you do that then you can do and import which should create all the tables and import any data you have.
After the data exists on the server then as far as the connection string, you just need to say the Data Source is the server ip address or host name and change your User ID and Pass to match that server.
If you need more details on any part of this process, post what tools your using and what your environment looks like and I would be more than happy to assist you.
In my opinion the best way to do that is to detach the db from one server(pc), copy the files to the second one and then attach them on the second server/pc.
To detach:
USE master;
GO
EXEC sp_detach_db #dbname = N'AdventureWorks2008R2';
GO
To attach:
USE master;
GO
CREATE DATABASE MyAdventureWorks
ON (FILENAME = 'C:\MySQLServer\AdventureWorks2008R2_Data.mdf'),
(FILENAME = 'C:\MySQLServer\AdventureWorks2008R2_Log.ldf')
FOR ATTACH;
GO
I have a Sql Server 2008 Express database file that's currently being used by an ASP.NET application, and I'm not sure how to query the database without taking the website down.
I'm unable to copy the database files (.mdf and .ldf files) to another directory, since they're in use by the web server. Also, if I attach the databases to an instance of the sql server (using the 'Create Database [DB name] on (filename = '[DB filename.mdf]') for attach;' command at the sqlcmd prompt), then the application pool user becomes unable to access the database (i.e. the webpages start producing http 500 errors. I think this might have to do with the username for the application pool becoming somehow divorced from the login credentials in the sql server database).
Any suggestions? I realize this is probably a newbie question, since it seems like a rather fundamental task. However, due to my inexperience, I really don't know what the answer is, and I'm pretty stumped at this point, since I've tried a couple of different things.
Thanks!
Andrew
if I attach the databases to an instance of the sql server (using the 'Create Database [DB name] on (filename = '[DB filename.mdf]') for attach;' command at the sqlcmd prompt),
Don't do this to a live database - it's attempting to be setup an MDF to be written to by two different databases...
Use Backup/Restore
As you've found, Attach/ReAttach requires the database to be offline - use the Backup/Restore functionality:
MSDN: Using SSMS to Backup the Database
MSDN: Using SSMs to Restore the Backup
Be aware that the backup/restore doesn't maintain logins (& jobs if you have any associated with the database) - you'll have to recreate & sync if using an account other than those with uber access.
Maybe Linked Server would work?
Another alternative would be to setup another SQL Server Express/etc instance on a different box, and use the Linked Server functionality to create a connection to the live/prod data. Use a different account than the one used for the ASP application...