tryCatch to Prevent R Shiny App Crushing on MySQL Connection Error - mysql

My Shiny App was crushing when wrong connection credentials were passed to the connection string. I then put my connection string within a tryCatch as follows:
,,,
ConnectToDb <- function(){
con <- tryCatch({
dbConnect(MySQL(),
user = input$db_user,
password = input$db_password,
dbname = input$db_name,
host = input$db_host,
port = input$db_port)
print("Connection made")
####
sql <- "SELECT * FROM PMSAnalytics;"
data <- dbGetQuery(con, sql)
# # Disconnect from the DB
dbDisconnect(con)
# # Convert to data.frame
data <- data.frame(data)
data$timestamp <- as_datetime(now())
data
####
}, error = function(e) {
message('Please confirm your login details')
print(e)
},
warning = function(w){
message('A warning has occured')
print(w)
return(NA)
}
)
}
,,,
Now the application does not crush, but however no error messages or warning are passed when wrong credentials are used and neither do I get a connection success. I have checked this site for similar questions, but I seem not to get any. Kindly assist with polishing the code.
Regards,
Chris

I work with showNotification, which directly shows a notification in the shiny UI, you could also use it for the connection success.
Also, Options for this are,
duration = 60 (in this case for 60 seconds)
closeButton = FALSE
For example:
error = function(e) {
showNotification(paste0(e), type = 'error')
}
warning = function(w){
showNotification(paste0(w), type = 'warning')
return(NA)
}

Related

MySQL Connection Error Handling with tryCatch

I have a R Shiny Application which uses MySQL as a datasource. When the application loads and the user logs into the app with their username and password, a database connection interface opens up where the user inputs their MySQL credentials. In order to prevent the app from crashing when the user enters the wrong MySQL connection credential, I am trying to use the following error handling.
# run when Load Data button is clicked
datapms <- eventReactive(input$pull_data, {
req(input$db_user,input$db_user,input$db_password,input$db_name,input$db_host,input$db_port)
progress <- Progress$new(session, min=1, max=15)
on.exit(progress$close())
progress$set(message = 'Pulling data from database',
detail = 'This message will disappear once completed.')
# establish a database connection
tryCatch({
con <- RMySQL::dbConnect(
RMySQL::MySQL(),
user = input$db_user,
password = input$db_password,
dbname = input$db_name,
host = input$db_host
)
}, error = function(e) {
debug_msg(e$message)
})
# construct the SQL statement
sql <- "SELECT * FROM pmsanalytics;"
# Fetch data
pmsanalytics <- tryCatch({
pmsanalytics <- dbGetQuery(conn = con, sql)
}, error = function(e) {
debug_msg(e$message)
})
### display debugging message in R (if local)
### and in the console log (if running in shiny)
debug_msg <- function(...) {
is_local <- Sys.getenv('SHINY_PORT') == ""
in_shiny <- !is.null(shiny::getDefaultReactiveDomain())
txt <- toString(list(...))
if (is_local) message(txt)
if (in_shiny) shinyjs::runjs(sprintf("console.debug(\"%s\")", text))
}
Initially this code was working, and the app was not crashing. However, now, when for example one enters the wrong connection credentials, i am getting the following error message:
Warning: Error in as.character: cannot coerce type 'closure' to vector of type 'character'
138: sprintf
136: debug_msg [C:\PMSAnalytics/app.R#107]
135: value[[3L]] [C:\PMSAnalytics/app.R#211]
134: tryCatchOne
133: tryCatchList
132: tryCatch
131: eventReactiveValueFunc [C:\PMSAnalytics/app.R#202]
Basically, the app crashes because there is no data which it is expecting to get, in other words the reactive datapms() data source it is expecting to get is empty.
Kind assist in reviewing my code to prevent app crashing.
Regards,
Chris

Python script won't quit because SSHTunnelForwarder hangs

Python:3.8.5
sshtunnel:0.2.1
mysqlclient:1.4.6
mysql-connector:2.2.9
I am using SSHTunnelForwarder to retrieve data from a Mysql database.
Here is the script I use to connect via SSH to the DB:
elif self._remote == 1:
with SSHTunnelForwarder(
(self._host, 22),
ssh_password = self._ssh_password,
ssh_username = self._ssh_login,
remote_bind_address = (self._remote_bind_address, 3306)) as server:
print('Connection:',server.local_bind_address)
cnx = MySQLdb.connect(host = '127.0.0.1',
port = server.local_bind_port,
user = self._db_user,
passwd = self._db_password,
db = self._db_name)
cursor = cnx.cursor()
res = pd.read_sql(request, con = cnx)
cursor.close()
cnx.close()
An example request could be in the following form:
request = 'SELECT * FROM conjunctions AS c LEFT JOIN events AS e ON e.eventId=c.eventId ORDER BY e.eventId;'
The script returns me a valid response, but will not exit to shell.
a threading.enumerate() will print this:
[<_MainThread(MainThread, started 139701046208320)>, <paramiko.Transport at 0x74850ac0 (unconnected)>, <paramiko.Transport at 0xae9e4e80 (unconnected)>]
I have found this issue relating to the same problem, however suggested solutions are not working for me.
Manually closing the tunnel with a server.stop() does not work.
Adding ssh_server.daemon_forward_servers = True as suggested in the issue mentioned above does not work.
Most of all, this problem appears approx 4/5 times the script is launched.
Any help to understand what is going on would be greatly appreciated.
Thank you.

How to use sparklyr spark_write_jdbc to connect to MySql

spark_write_jdbc(members_df,
name = "Mbrs",
options = list(
url = paste0("jdbc:mysql://",mysql_host,":",mysql_port,"/",dbname),
user = mysql_user,
password = mysql_password),
mode = "append")
Results in the following exception:
Error: java.sql.SQLException: No suitable driver
at java.sql.DriverManager.getDriver(DriverManager.java:315)
The .jar file is in a folder on the server where RStudio is running, config details below. We're able to access MySql via the RMySql package so MySql is working and accessible.
config$`spark.sparklyr.shell.driver-class-path` <- "/dev/shm/temp/mysql-connector-java-5.1.44-bin.jar"
Even if the question is different, I think the answer still applies also to this:
How to use a predicate while reading from JDBC connection?
Code to connect to JDBC MySQL through sparklyr (I made some slight changes to simplify the code a bit, written by Jake Russ)
library(sparklyr)
library(dplyr)
config <- spark_config()
#config$`sparklyr.shell.driver-class-path` <- "E:\\spark232_hadoop27\\jars\\mysql-connector-java-5.1.47-bin.jar"
#in my case, using RStudio and Sparkly this seemed to be optional
sc <- spark_connect(master = "local")
db_tbl <- spark_read_jdbc(sc,
name = "table_name",
options = list(url = "jdbc:mysql://localhost:3306/schema_name",
user = "root",
password = "password",
dbtable = "table_name"))

Multiple DB connection in R

I was wondering if someone could help with this annoying issue.
I'm trying to create/make multiple connections to different database.
I have a data.frame with 3 connection credentials named conf - It works if I manually enter the connections variable like so:
conn <- dbConnect(MySQL(), user=conf$user, password=conf$passws, host=conf$host, dbname=conf$db)
which ends up creating a single connection.
However, what I want is to be able to refer to the connection as:
conf$conn <- dbConnect(MySQL(), user=conf$user, password=conf$passws, host=conf$host, dbname=conf$db)
here is the error message I'm getting.
Error in rep(value, length.out = nrows) :
attempt to replicate an object of type 'S4'
I think the problem is how I'm adding conf$conn
I used a combination of the pool and config package to solve a similar problem to set up a number of simultaneous PostgreSQL connections. Note that this solution needs a config.yml file with the connection properties for db1 and db2.
library(pool)
library(RPostgreSQL)
connect <- function(cfg) {
config <- config::get(config = cfg)
dbPool(
drv = dbDriver("PostgreSQL", max.con = 100),
dbname = config$dbname,
host = config$host,
port = config$port,
user = config$user,
password = config$password
)
}
conn <- lapply(c("db1", "db2"), connect)

Using the LDAvis package in R to create a gist file of the result

I'm using LDAvis for topic modeling and trying to use the as.gist option to create a gist. When serVis executes there is a timeout in curl::curl_fetch_memory after about 10 seconds. If I immediately execute serVis again I get a different error 'Problems parsing JSON' and from then on whenever serVis is run that same error recurs.
If I start all over with a fresh workspace the same behavior occurs. The first time serVis is run, curl::curl_fetch_memory times out after about 10 seconds. Subsequent executions return 'Problems parsing JSON'.
If I don't use the as.gist option it works fine, but of course doesn't create a gist.
Very rarely, it works and a gist is created. If I change parameters to reduce the size of the JSON object it usually works, which makes me think it may be related to size.
I have explored the various RCurlOptions timeout settings. Currently, they are set as
options(RCurlOptions = list(cainfo = system.file("CurlSSL", "cacert.pem",
package = "RCurl"),
connecttimeout = 300, timeout = 3000,
followlocation = TRUE, dns.cache.timeout = 300))
Below is a console listing with debug set on curl::curl_fetch_memory.
> json <- createJSON(phi = cases$phi,
+ theta = cases$theta,
+ doc.len .... [TRUNCATED]
> serVis(json, open.browser = TRUE, as.gist = TRUE, description = 'APM Community')
debugging in: curl::curl_fetch_memory(url, handle = handle)
debug: {
output <- .Call(R_curl_fetch_memory, url, handle)
res <- handle_response_data(handle)
res$content <- output
res
}
Browse[2]> output <- .Call(R_curl_fetch_memory, url, handle)
Error: Timeout was reached
Browse[2]> output <- .Call(R_curl_fetch_memory, url, handle)
Browse[2]> rawToChar(output)
[1] "{\"message\":\"Problems parsing JSON\",\"documentation_url\":\"https://developer.github.com/v3\"}"
Browse[2]>
.
.
exiting from: curl::curl_fetch_memory(url, handle = handle)
Error: Problems parsing JSON
Any hints on how to debug this problem?