I want to connect RStudio to a database in PostgreSQL. So firstly following the instructions I modified the odbcinst.ini file:
[PostgreSQL Driver]
Driver = /usr/local/lib/psqlodbcw.so
Ok, so now appears a PostgreSQL selectable in connection. And then I tried to make the connection:
con <- dbConnect(odbc::odbc(),
.connection_string = "Driver={PostgreSQL Driver};",
dbname = 'name',
host = 'host',
user = 'user',
password = 'pass',
port = 5432,
timeout = 10)
But it returns me an error:
rror: nanodbc/nanodbc.cpp:983: 00000: could not connect to server: No such file or directory
Is the server running locally and accepting
connections on Unix domain socket "/tmp/.s.PGSQL.5432"?
I have tried so far:
drv <- dbDriver("RPostgreSQL")
con <- dbConnect(drv,
dbname = 'name',
host = 'host',
user = 'user',
password = 'pass',
port = 5432)
That works but I'm unable to navigate the database (I mean, to see the tables and connection status) in RStudio.
My question is: Should I change my driven in odbcinst.ini? What would be the .so file? Any help pointing what to do will be greatly appreciated. By the way I'm running on Mac, and the host is in Amazon.
Perhaps RPostgres can help you out
con <- RPostgres::dbConnect(RPostgres::Postgres(),
dbname = 'name',
host = 'host',
user = 'user',
password = 'pass',
port = 5432)
After some trial and error this worked for me:
con <- dbConnect(odbc::odbc(),
Driver = "PostgreSQL Driver",
Database = 'name',
Server = 'host',
UID = 'user',
PWD = 'pass',
Port = 5432,
timeout = 10)
Voila, now I can see the tables in the database.
Related
I have a connection to a mysql server like this:
mydb <- DBI::dbConnect(
drv = MySQL(),
host = "host",
port = 1111,
user = "user_1",
password = "password",
dbname = "database_name"
)
and then I do queries to that data table using this code
query1 <- fetch(dbSendQuery(mydb, "select * from table_1"), n = Inf)
so the result is that I have a query1 table in the R environment.
Now I have other databases in SQL Server, so I'm trying to do the same. I'm establishing the connection doing this:
con <- dbConnect(odbc(),
Driver = "SQL Server",
Server = "server",
Database = "database_2",
UID = "user_2",
PWD = "password",
Port = 2222)
and it seems that works, because in the Connection tab appears the database, but when I navigate and try to see the data an error occurs. Besides this, I'm looking for functions that do the same like the previous (fetch with dbSendQuery), having this way the data frames available in the environment.
I finally solved the problem using this code:
con <- dbConnect(odbc(),
Driver = "ODBC Driver 17 for SQL Server",
Server = "server",
Database = "database_2",
UID = "user_2",
PWD = "password",
Port = 2222)
So the problem was in the Driver.
In my shiny application, in global.R I have defined an odbc connection as follow :
con <- dbConnect(odbc(),
DSN = 'abc',
Database = 'xxx',
UID = rstudioapi::askForPassword("Database user"),
PWD = rstudioapi::askForPassword("Database password")
)
The app is working when I try it from RStudio IDE, but it is not when I deploy the app on the server.
The error is :
Error: RStudio not running
Execution halted
But if I change the odbc connection to :
con <- dbConnect(odbc(),
DSN = 'abc',
Database = 'xxx',
UID = "myuser",
PWD ="mypass"
)
The app will work properly.
Any Idea how that could fix to avoid using the username / pass in the code ?
I am trying to access some tables on Redshift with shinyR that are under a schema, I can connect to a table that are not under a schema using library(RPostgresSQL) so I know this part is working:
pconn_r <- dbConnect(RPostgres::Postgres(),
host = "xxxxxxxxxxxx",
port = "5439",
user = "rcd_admin",
password = "xxxxxxx",
dbname = "xxxx"
)
but i'm unable to access my table fr__synapps_drug__outpatient_index under the schema synapps with this command :
sql_command <- "Select cip13_code,cis_label,presentation_label,brand,period,hco_code,hco_label,hco_code_type,hco_city,bse,rem,unit from synapps.fr__synapps_drug__outpatient_index"
outpatient <- dbSendQuery(pconn_r, sql_command)
I found a solution:
myRedshift <- DBI::dbConnect(RPostgreSQL::PostgreSQL(),
dbname = 'oip',
host = 'xxxx',
port = 5439,
user = "xxxadmin",
password = "xxx")
cis_has_bdpm <-data.frame( dbGetQuery(myRedshift, "select * from synapps.fr__synapps_drug__has_index"))
I change the way to connect to Redshift and it's working, but the loading of the data is very slow
I connect to a mongodb server using port forwarding like this:
ssh -i key.pem -Nf -L 27018:xx.xxx.xxx.xxx:27017 ubuntu#xx.xxx.xxx.xxx
mongo -u user -p pass --authenticationDatabase "db" --port 27018
Then I run R to connect and query the database:
library(RMongo)
mg1 <- mongoDbConnect(dbName = 'db', host = 'xx.xxx.xxx.xxx', port = 27018)
auth <- dbAuthenticate(rmongo.object = mg1, username = 'user', password = 'pass')
This gives me an error while authentication:
Error in .jcall(rmongo.object#javaMongo, "Z", "dbAuthenticate", username, :
com.mongodb.MongoException$Network: IOException authenticating the connection
Without port forwarding, my credentials work:
library(RMongo)
mg1 <- mongoDbConnect(dbName = 'db', host = 'xx.xxx.xxx.xxx', port = 27017)
auth <- dbAuthenticate(rmongo.object = mg1, username = 'user', password = 'pass')
How do I set my port in mongoDbconnect?
Thanks!
Ok, this works. No need to put the host because now we are mapped to the localhost:
library(RMongo)
mg1 <- mongoDbConnect(dbName = 'db', host = 'localhost', port = '27018')
auth <- dbAuthenticate(rmongo.object = mg1, username = 'user', password = 'pass')
I'm trying to connect to remote publicly-accessible MySQL server EnsEMBL public server using RMySQL, but when I try to list the tables, an error occurs:
library(RMySQL)
mydb = dbConnect(MySQL(),
user = 'anonymous',
port = 5306,
host = 'asiadb.ensembl.org')
dbListTables(mydb)
Error in .local(conn, statement, ...) :
could not run statement: No database selected
Is there a a way to find out the name? Or Am I making a completely different mistake altogether?
You have to specify the name of the db in the dbConnect call. e.g. :
mydb = dbConnect(MySQL(),
user = 'anonymous',
port = 5306,
host = 'asiadb.ensembl.org',
db = 'homo_sapiens_core_83_38')
dbListTables(mydb)
It is weird that database = 'testdb' executed with dbExecute in R
db <- dbConnect(RMySQL::MySQL(),
user = 'root',
password = 'pwd123',
host = 'localhost',
database = 'testdb'
)
dbExecute(db, MySQLStatement) # Executed Without Error
But when used dbListTables(db) showing no databases selected.
Changed database into db worked as expected
db <- dbConnect(RMySQL::MySQL(),
user = 'root',
password = 'pwd123',
host = 'localhost',
db = 'testdb'
)