I'm trying to access a SQL Server on a local intranet with R, where R is loaded in a docker file with R-base.
On my desktop, I create a ODBC driver and it recognizes my windows credentials with the following:
odbcDriverConnect('driver={SQL Server};server=<serverName>;database=<dbName>;trusted_connection=yes')
Using R-base, after a lot of trial and error I was able to get RODBC installed, but I have no idea how to connect to this server.
Warning messages:
[RODBC] ERROR: state 01000, code 0, message [unixODBC][Driver Manager]Can't open lib 'SQL Server' : file not found
The DockerFile, which was built with a lot of trial and error. I'm sure much of it is redundant. Also I exposed ports which I found doing some research but I have no idea if they are needed to be exposed.
FROM openanalytics/r-base
# system libraries of general use
RUN apt-get update && apt-get install -y \
sudo \
libcairo2-dev \
libxt-dev \
libcurl4-gnutls-dev \
libssl-dev \
libssh2-1-dev \
libssl1.0.0
# RODBC
RUN apt-get update && \
apt-get install -y --no-install-recommends \
unixodbc \
unixodbc-dev \
unixodbc \
unixodbc-dev \
r-cran-rodbc \
apt-transport-https \
libssl-dev \
libsasl2-dev \
openssl \
curl \
unixodbc \
gnupg \
libc6 libc6-dev libc6-dbg
RUN curl https://packages.microsoft.com/keys/microsoft.asc | apt-key add -
RUN curl https://packages.microsoft.com/config/ubuntu/18.04/prod.list > /etc/apt/sources.list.d/mssql-release.list
#RUN curl https://packages.microsoft.com/config/ubuntu/19.10/prod.list > /etc/apt/sources.list.d/mssql-release.list
RUN apt-get update -y
RUN ACCEPT_EULA=Y apt-get install -y msodbcsql17 unixodbc-dev mssql-tools
EXPOSE 3838
EXPOSE 8787
Once I build the file, I enter R studio and use install.packages("RODBC")
How can I connect to the SQL server from the docker file?
----------Update
after creating a docker container with Ubuntu, I found that I was not able to ping the server name. I was however, able to ping the server ip address.
I modified the search string to ping the ip address, and changed the driver, as follows:
odbcDriverConnect('driver={ODBC Driver 17 for SQL Server};server=<serverName>;database=<dbName>;trusted_connection=yes')
This still did not work.
I could not figure out how to connect to the database with the Windows credentials of the docker host inside of the docker virtual machine.
I had to make a username and password for the database and connect with that.
I think if you change your driver to FreeTDS this will work. R doesn't support Sql Server drivers unless its a pro plan.
Related
I have the following dockerfile:
FROM rocker/tidyverse:3.5.2
RUN apt-get update
# System dependices for R packages
RUN apt-get install -y \
git \
make \
curl \
libcurl4-openssl-dev \
libssl-dev \
pandoc \
libxml2-dev \
unixodbc \
libsodium-dev \
tzdata
# Clean up package installations
RUN apt-get clean
# ODBC system dependencies
RUN apt-get install -y gnupg apt-transport-https
RUN curl https://packages.microsoft.com/keys/microsoft.asc | apt-key add -
RUN curl https://packages.microsoft.com/config/debian/9/prod.list > /etc/apt/sources.list.d/mssql-release.list
RUN apt-get update
RUN ACCEPT_EULA=Y apt-get install msodbcsql17 -y
# Install renv (package management)
ENV RENV_VERSION 0.11.0
RUN R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"
RUN R -e "remotes::install_github('rstudio/renv#${RENV_VERSION}')"
# Specify USER for rstudio session
ENV USER rstudio
COPY ./renv.lock /renv/tmp/renv.lock
WORKDIR /renv/tmp
RUN R -e 'renv::consent(provided = TRUE)'
RUN R -e "renv::restore()"
WORKDIR /home/$USER
I use this image to recreate environments for R scripting purposes. This was working for a number of months up until the end of September when I started getting:
Error in curl::curl_fetch_memory(url, handle = handle) :
SSL certificate problem: certificate has expired
This occured when using GET request to query a website. How do I update my certificate now and in the future to avoid certificates expiring...I do not want to use the "config(ssl_verifypeer = FALSE)" workaround.
This happened to me too. Any chance you are working on MacOS or Linux based machine? It seems to be a bug:
https://security.stackexchange.com/questions/232445/https-connection-to-specific-sites-fail-with-curl-on-macos
ca-certificates Mac OS X
SSL Certificates - OS X Mavericks
Instead of adjusting the certificates as is suggested here, you can simply set R to not verify the peer. Just add the following line to the beginning of your code.
httr::set_config(config(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE))
I am trying to use the odbc package to connect to a SQL Server database for my application. When I run it locally, for example, on Rstudio, it does work just fine but when I try to run it on shiny proxy, or in a container directly, it doesn't work.
Here is the code of the dockerfile
FROM openanalytics/r-base
#update all packages
RUN apt-get update
#upgrade
RUN apt-get upgrade -y
#install additional packages
RUN apt install gpg-agent -y unixodbc apt-utils curl unixodbc-dev \
sudo \
pandoc \
pandoc-citeproc \
libcurl4-gnutls-dev \
libcairo2-dev \
libxt-dev \
libssl-dev \
libssh2-1-dev \
libssl1.1 \
libmpfr-dev \
libxml2-dev
# R packages
RUN R -e "install.packages(c('shiny', 'rmarkdown'), repos='https://cloud.r-project.org/')"
RUN R -e "install.packages('Rmpfr', repos='https://cloud.r-project.org/')"
RUN R -e "install.packages('shinydashboard', repos='https://cloud.r-project.org/')"
RUN R -e "install.packages('xml2')"
RUN R -e "install.packages('rvest')"
RUN R -e "install.packages('plotly', repos='https://cloud.r-project.org/')"
RUN R -e "install.packages('reactable', repos='https://cloud.r-project.org/')"
RUN R -e "install.packages('tidyverse')"
RUN R -e "install.packages('DBI')"
#get msodbcsql17 and install it
RUN curl https://packages.microsoft.com/keys/microsoft.asc | apt-key add -
RUN curl https://packages.microsoft.com/config/ubuntu/20.04/prod.list > /etc/apt/sources.list.d/mssql-release.list
RUN apt-get update -y
RUN ACCEPT_EULA=Y apt-get install -y msodbcsql17
RUN ACCEPT_EULA=Y apt-get install -y mssql-tools
#install packaes needed for running the app
RUN R -e "install.packages(c('odbc', 'data.table'))"
# copy the app to the image
RUN mkdir /root/app_src
COPY app_src /root/app_src
COPY Rprofile.site /usr/lib/R/etc/
EXPOSE 3838
CMD ["R", "-e", "shiny::runApp('/root/app_src')"]
And here is the line where I connect to the data base
db_Inv <- DBI::dbConnect(odbc::odbc(), Driver = "ODBC Driver 17 for SQL Server", Server = "10.200.16.8", Database = "Investigacion", UID = "*****", PWD = "*****", Port = 1433)
As you can see, on the Dockerfile there are some lines about installing ms sql server drivers. I run the same lines on rstudio console and everything work just fine.
The problem when I run the code on shinyproxy or in the container directly is this:
Warning: Error in : nanodbc/nanodbc.cpp:1021: 00000: [Microsoft][ODBC Driver 17 for SQL Server]TCP Provider: Error code 0x2746
[Microsoft][ODBC Driver 17 for SQL Server]Client unable to establish connection [Microsoft][ODBC Driver 17 for SQL Server]Invalid connection string attribute
57:
Error : nanodbc/nanodbc.cpp:1021: 00000: [Microsoft][ODBC Driver 17 for SQL Server]TCP Provider: Error code 0x2746 [Microsoft][ODBC Driver 17 for SQL Server]Client unable to establish connection
[Microsoft][ODBC Driver 17 for SQL Server]Invalid connection string attribute
Does anyone have a suggestion?
Thanks!
I am deploying simple plumber API in Azure container which executes simple SQL query and returns results. Here is my Dockerfile.
# start from the rocker/r-ver:4.0.2 image
# minor change to one branch to test deployment
FROM rocker/r-ver:4.0.2
# install the linux libraries needed for plumber
RUN apt-get update -qq && apt-get install -y \
libssl-dev \
libcurl4-gnutls-dev \
libsodium-dev \
unixodbc-dev \
r-cran-rodbc \
curl\
libxml2-dev
# libiodbc2-dev
# We need to update Dockerfile to install ODBC Driver 17 for SQL Server for
# Ubuntu 20.04 or different version
# here is link: https://learn.microsoft.com/en-us/sql/connect/odbc/linux-mac/installing-the-microsoft-odbc-driver-for-sql-server?view=sql-server-ver15#ubuntu17
RUN curl https://packages.microsoft.com/keys/microsoft.asc | apt-key add -
RUN curl https://packages.microsoft.com/config/ubuntu/20.04/prod.list > /etc/apt/sources.list.d/mssql-release.list
RUN apt-get update
RUN ACCEPT_EULA=Y apt-get install -y msodbcsql17
RUN ACCEPT_EULA=Y apt-get install -y mssql-tools
RUN echo 'export PATH="$PATH:/opt/mssql-tools/bin"' >> ~/.bash_profile
RUN echo 'export PATH="$PATH:/opt/mssql-tools/bin"' >> ~/.bashrc
# RUN source /etc/bash.bashrc
RUN mkdir -p ~/application
# copy everything from the current directory into the container
COPY "/" "application/"
# I probably do not even have to set up WORKDIR
WORKDIR "application/"
# open port 80 to traffic
EXPOSE 80
# install plumber
RUN R -e "install.packages('plumber')"
RUN R -e "install.packages('renv')"
RUN R -e "install.packages('RODBC')"
RUN R -e 'renv::restore()'
# when the container starts, start the main.R script
ENTRYPOINT ["Rscript", "execute_plumber.R"]
API works fine. However, when I connect to container, run R and execute library(RODBC) I get back error about library not found. This is puzzling since it is already mentioned in Dockerfile, but maybe it has something to do with renv. I proceed with installation install.packages('RODBC') and it generates error which I can fix by running apt-get install unixodbc-dev and apt-get install r-cran-rodbc. Those lines are again already present in Dockerfile. Then when I try to connect to SQL server I get error about driver. And again I can fix it by re-executing lines from Dockerfile (related to SQL Server 17 driver).
So I am puzzled why I need to re-execute some items already present in Dockerfile. Or maybe when I click "Connect" in Azure it actually connects me to host and not to container?
I am trying to deploy my Shiny app on my own server, but I cannot solve this issue. This is my docker image
FROM rocker/tidyverse
## App folder
WORKDIR /home/admin/shinyAppCovid/
ADD /shinyApp /shinyApp/
ADD /dependencias.txt /usr/local/bin/
RUN apt-get update && apt-get install -y \
sudo \
pandoc \
pandoc-citeproc \
libcurl4-gnutls-dev \
libcairo2-dev \
libxt-dev \
libssl-dev \
libssh2-1-dev
# expose port
EXPOSE 8080
# Download and install library
RUN R -e 'install.packages(read.csv("/usr/local/bin/dependencias.txt")[,1], depencencies=TRUE, repos="http://cran.rstudio.com/")'
# run app on container start
CMD ['/usr/bin/R', "-e", "shiny::runApp("/shinyApp/shiny", host = '0.0.0.0', port = 8080)"]
The problem is that when i a try to run a container this is what i have
/bin/sh: 1: [/usr/bin/R,: not found
I changed the last line for jus R and is not working I am still having the same issue, How can I do?
I've setup a Shiny App using docker shiny image and all works well until I attempt to call API using httr package. From what I can get I'm unable to access internet from the App as I get the Timeout message from multiple sites, and verified the work from going through web browser. Wondering what setting I need to change?
From the RStudio Console within the App:
> library(httr)
> r <- GET("http://httpbin.org/get")
Error in curl::curl_fetch_memory(url, handle = handle) :
Timeout was reached: [httpbin.org] Connection timed out after 10000 milliseconds
Here is my DockerFile:
FROM rocker/tidyverse
RUN apt-get update
RUN apt-get install -y libpq-dev
RUN R -e 'install.packages("RPostgres")'
RUN R -e 'install.packages("DT")'
I just needed to add the following libraries in Dockerfile and worked
RUN apt-get install -y libpq-dev \
libssl-dev \
libcurl4-openssl-dev \
curl \
sudo \
pandoc \
pandoc-citeproc \
libcairo2-dev \
libxt-dev \
libssl-dev \
libssh2-1-dev