I receive the following error...
Error in b_wincred_i_get(target) :
Windows credential store error in 'get': Element not found.
...when running the following script in R v3.5.1 (R Studio v1.1.456) and keyring v1.1.0. I'm attempting this on a new setup so not sure if this could be as simple as a firewall issue or the like. The script errors out when attempting to get the password (key_get(json_data$service, json_data$user)). I've tried manually plugging in the service and username into the key_get method (instead of using the variables from the config file) but get the same error. The config file is a json file that holds all of the connection details except the password, which obviously gets retrieved from the Windows Credentials Vault. Any help in figuring out a fix for this is greatly appreciated.
library(RJDBC)
library(keyring)
library(jsonlite)
postgres.connection <- function(json_data){
print("Creating Postgres driver...")
pDriver <- JDBC(driverClass=json_data$driver, classPath="C:/Users/Drivers/postgresql-42.2.4.jar")
print("Connecting to Postgres...")
server <- paste("jdbc:postgresql://", json_data$host, ":", json_data$port, "/", json_data$dbname, sep="")
pConn <- dbConnect(pDriver, server, json_data$user, key_get(json_data$service, json_data$user))
return(pConn)
}
json_data <- fromJSON("C:/Users/Configs/Config.json", simplifyVector = TRUE, simplifyDataFrame = TRUE)
json_data_connection <- json_data$postgres$local_read
pc <- postgres.connection(json_data_connection)
You mentioned it's a new setup. Is the password already in credentials? To check, go to 'Control Panel'>'User Accounts'>'Credential Manager'>'Windows Credentials', is it under 'Generic Credentials'?
I can get the same error by running:
key_get('not-valid-service', 'some-user')
Related
I'm using the gmailr package for sending emails from a r script.
Locally it's all working fine, but when I try to run this during a docker build step in google cloud I'm getting an error.
I implemented it in the following way described here.
So basically, locally the part of my code for sending emails looks like this:
gm_auth_configure(path = "credentials.json")
gm_auth(email = TRUE, cache = "secret")
gm_send_message(buy_email)
Please note, that I renamed the .secret folder to secret, because I want to deploy my script with docker in gcloud and didn't want to get any unexpected errors due to the dot in the folder name.
This is the code, which I'm now trying to run in the cloud:
setwd("/home/rstudio/")
gm_auth_configure(path = "credentials.json")
options(
gargle_oauth_cache = "secret",
gargle_oauth_email = "email.which.was.used.to.get.secret#gmail.com"
)
gm_auth(email = "email.which.was.used.to.get.secret#gmail.com")
When running this code in a docker build process, I'm receiving the following error:
Error in gmailr_POST(c("messages", "send"), user_id, class = "gmail_message", :
Gmail API error: 403
Request had insufficient authentication scopes.
Calls: gm_send_message -> gmailr_POST -> gmailr_query
I can reproduce the error locally, when I do not check the
following box.
Therefore my first assumption is, that the secret folder is not beeing pushed correctly in the docker build process and that the authentication tries to authenticate again, but in a non interactive-session the box can't be checked and the error is thrown.
This is the part of the Dockerfile.txt, where I'm pushing the files and running the script:
#2 ADD FILES TO LOCAL
COPY . /home/rstudio/
WORKDIR /home/rstudio
#3 RUN R SCRIPT
CMD Rscript /home/rstudio/run_script.R
and this is the folder, which contains all files / folders beeing pushed to the cloud.
My second assumption is, that I have to somehow specify the scope to use google platform for my docker image, but unfortunately I'm no sure where to do that.
I'd really appreciate any help! Thanks in advance!
For anyone experiencing the same problem, I was finally able to find a solution.
The problem is that GCE auth is set by the "gargle" package, instead of using the "normal user OAuth flow".
To temporarily disable GCE auth, I'm using the following piece of code now:
library(gargle)
cred_funs_clear()
cred_funs_add(credentials_user_oauth2 = credentials_user_oauth2)
gm_auth_configure(path = "credentials.json")
options(
gargle_oauth_cache = "secret",
gargle_oauth_email = "sp500tr.cloud#gmail.com"
)
gm_auth(email = "email.which.was.used.for.credentials.com")
cred_funs_set_default()
For further references see also here.
I'm trying to automate data download from db using RJDBC using a for loop. The database im using automatically closes the connection after every 10mins, so what i want to do is somehow catch the error, remake the connection, and continue the loop. In order to do this i need to capture the error somehow, the problem is, it is not an r error so none of the commands trycatch and similar works. I just get a text on the console telling me:
Error in .jcheck() : No running JVM detected. Maybe .jinit() would help.
How do i handle this in terms of:
if (output == ERROR) {remake connection and run dbQuery} else {run dbQuery}
thanks for any help
You could use the pool package to abstract away the logic of connection management.
This does exactly what you expect regarding connection management with DBI.
It should work with RJDBC which is an implentation of DBI, but I didn't test it with this driver.
libray(pool)
library(RJDBC)
conn <- dbPool(
drv = RJDBC::JDBC(...),
dbname = "mydb",
host = "hostadress",
username = "test",
password = "test"
)
on.exit(poolClose(conn))
dbGetQuery(conn, "select... ")
I have a SQL Server database to which I can connect with my user and this password: "testspecialcharacters_¤" through MS Studio without problems. We are using windows authentication to connect to the server.
However I cannot connect to it through my R Shiny app. I cannot give the exact server, database and user names but this is very close to the code I am using:
library(RODBCext)
ch <- odbcDriverConnect("DSN=test;database=test_db;UID=test_user;PWD=testspecialcharacters_¤")
data <- sqlQuery(ch,"select * from test_db.general.test_tbl")
I receive the following error:
[RODBC] ERROR: state 42000, code 18452, message [unixODBC][FreeTDS][SQL Server]Login failed. The login is from an untrusted domain and cannot be used with Windows authentication.
[RODBC] ERROR: state 08001, code 0, message [unixODBC][FreeTDS][SQL Server]Unable to connect to data source
ODBC connection failed
I have to mention that the same code works for passwords without that special character. From experience we have found out that "-" and "!" seem to work. However "#" and "¤" do not work. We have not tried all the potential special characters, only these few.
Based on different other posts online I have tried the following, with no success:
ch <- odbcDriverConnect("DSN=test;database=test_db;UID=test_user;PWD=testspecialcharacters_¤", DBMSencoding = "UTF-8")
ch <- odbcDriverConnect("DSN=test;database=test_db;UID=test_user;PWD=testspecialcharacters_¤", DBMSencoding = "UTF-8-BOM")
ch <- odbcDriverConnect("DSN=test;database=test_db;UID=test_user;PWD=testspecialcharacters_¤", DBMSencoding = "latin1")
ch <- odbcDriverConnect("DSN=test;database=test_db;UID=test_user;PWD={testspecialcharacters_¤}")
ch <- odbcDriverConnect("DSN=test;database=test_db;UID=test_user;PWD='testspecialcharacters_¤'")
I am using RStudio Pro with UTF-8 default encoding.
Does anybody know how to escape the special characters used in the password string? Or if a different way of connecting to the database is needed.
The best way is to use basic escaping like this. But you have to test it on your machine, because setting correct encoding between your machine and database is really hard.
x <- "¤"
y <- "\u00A4"
identical(x, y) # true
And link for table
https://www.utf8-chartable.de/
I am trying to follow the "Getting started with MongoDB in R" page to get a database up and running. I have mongoDB installed in my PATH so I am able to run mongod from the terminal and open an instance. Though when I open an instance in the background and try running the following commands in R:
library(mongolite)
m <- mongo(collection = "diamonds") #diamonds is a built in dataset
It throws an error after that last statement saying:
Error: No suitable servers found (`serverSelectionTryOnce` set): [Failed to resolve 'localhost']
How do I enable it to find the connection I have open? Or is it something else? Thanks.
It could be that mongolite is looking in the wrong place for the local server. I solved this same problem for myself by explicitly adding the local host address in the connection call:
m <- mongo(collection = "diamonds", url = "mongodb://127.0.0.1")
I am interested in opening an Excel 2007 file in R 2.11.1 using RODBC. The Excel file resides in the shared documents page of a MOSS2007 website. I currently download the .xlsx file to my hard drive and then import to R using the following code:
library(RODBC)
con<-odbcConnectExcel2007("C:/file location/file.xlsx")
data<-sqlFetch(con, "worksheet name")
close(con)
When I type in the web url for the document into the odbcConnectExcel2007 connection, an error message pops up with:
ODBC Excel Driver Login Failed: Invalid internet Address.
followed by the following message in my R console:
ERROR: Could not SQLDriverConnect
Any insights you can provide would be greatly appreciated.
Thanks!
**UPDATE**
The site I am attempting to download from is password protected. I tried another method using the method 'getUrl' in the package RCurl:
x = getURL("http://website.com/file.xlsx", userpwd = "uname:pw")
The error that I receive is:
Error in curlPerform(curl = curl, .opts = opts, .encoding = .encoding) :
embedded nul in string: 'PK\003\004\024\0\006\0\b\0\0\0!\0dA»ï\001\0\0O\n\0\0\023\0Ò\001[Content_Types].xml ¢Î\001( \0\002\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\
I have no idea what this means. Any help would be appreciated. Thanks!
Two solutions worked for me.
If you do not need to automate the script that pulls the data, you can map a network drive pointing to the sharepoint folder from which you want to extract the Excel document.
If you need to automate a script to pull the Excel file every couple of minutes, I recommend sending your authentication credentials in a request that automatically saves the file to a local drive. From there you can read it into R for further data wrangling.
library("httr")
library("openxlsx")
user <- <USERNAME>
password <- <PASSWORD>
url <- "https://sharepoint.company/file_to_obtain.xlsx"
httr::GET(url,
authenticate(user, password, type="ntlm"),
write_disk("C:/tempfile.xlsx", overwrite = TRUE))
df <- openxlsx::read.xlsx("C:/tempfile.xlsx")
You can obtain the correct URL to the file by clicking on the sharepoint location and removing "?Web=1" after the file ending (xlsx, xlsb, xls,...). USERNAME and PASSWORD are usually windows credentials. It helps storing them in a key manager (such as:
library("keyring")
keyring::key_set_with_value(service = "Windows", username = "Key", password = <PASSWORD>)
and then authenticating via
authenticate(user, kreyring::key_get("Windows", "Key"), type="ntlm")
in some instances it may be sufficient to pass
authenticate(":", ":", type="ntlm")
if only your Windows credentials are required and the code is running from your machine.