---
# System prepended metadata

title: RStudio Server (ongoing questions/issues)

---

# RStudio Server (ongoing questions/issues)

## DB Connections 

When establishing a connection with the CDMRESTRICTED My SQL database, we've run into problems installing the `odbc` package. 

I was able to install the `DBI` and `odbc` packages: 

```r=
# packages for data manipulation/file system 
library(tidyverse)
library(fs)

# install DBI
renv::install("DBI")
library(DBI)

# install odbc (from other repo)
options(repos = "https://aceshiny-dev.bmrn.com/rspm/full-cran-as-of-2021-11-01/__linux__/centos7/latest")
renv::install("odbc")
library(odbc)

# update renv
renv::snapshot()

# list servers 
sort(unique(odbc::odbcListDrivers()[[1]]))

# list servers 
sort(unique(odbc::odbcListDrivers()[[1]]))

# Now i can see the listed drivers 
# "Athena"     "BigQuery"   "Cassandra"  "Hive"       "Impala"     
# "MongoDB"    "MySQL"      "Netezza"  "Oracle"     "PostgreSQL" "Redshift"
# "Salesforce" "SQLServer"  "Teradata

# test DB connection 
dbconn <- dbConnect(odbc::odbc(),
                    Driver = "SQLServer",
                    Server = "172.24.98.38",
                    Database = "cdmrestricted" , 
                    UID = "srv_cdm_restricted",
                    PWD = rstudioapi::askForPassword("Database password"),
                    Port = 1433)
```

However, after trying to connect with using my BioMarin credentials, I am still receiving the following error:
 
```r=
# Error: nanodbc/nanodbc.cpp:1021: 00000: [unixODBC][RStudio][SqlServer]
#  (18456) Login failed for user 'srv_cdm_restricted'.
```

Follow up with Dinh on the username/password. 

## `htmltools` installation issue

- [x] This issue went away when I used renv::update() to update the packages in the `renv/` folder and lockfile. The R Markdown vignette was able to render. 

## Completeness listing (UAT)

I've moved the completeness listing application into the UAT server, and it lives here on GitLab: 

https://git.bmrn.com/Martin.Frigaard/completeness-listing-shiny

I created a new project for this application in RStudio Server using **Project** > **New Project** > **Version Control** > **Git** 

Then entered the repository url and cloned the project. 

The application development form: 

[2022-06-15-completeness-app-dev-form](https://bmrn-my.sharepoint.com/:w:/p/ma904058/EWEzT8nBo9xNk7S4Fb7BkdIBSC6XsXEXvfkPwgwClxtQXw?e=zCL5y0)

The wireframe is available [here](https://bmrn-my.sharepoint.com/:u:/p/ma904058/Ee7D5Vj8YZlBp_G-lGP5adkBCezW2nYBUeoF3hHNQvXyfQ?e=s5Le9r)

### Data Access


Ask for permission to create a folder in SAS QA: \\sassysqa.bmrn.com

i.e., we need two folders in the QA folder: 

```bash=
# 270-301 QA
\\sassysqa.bmrn.com\cdm\cdmdev\bmn270\hemoa\270301\csrblinded\output\clin\rshiny
# 270-303 QA
\\sassysqa.bmrn.com\cdm\cdmdev\bmn270\hemoa\270303\csrblinded\output\clin\rshiny
```

We need to create folders in SAS QA that are identical the folders in production: 

```bash=
# 270-301 Production
\\sassysprd.bmrn.com\cdm\cdmdev\bmn270\hemoa\270301\csrblinded\output\clin\rshiny
# 270-303 Production
\\sassysprd.bmrn.com\cdm\cdmdev\bmn270\hemoa\270303\csrblinded\output\clin\rshiny
```

Both of these have completeness listings in them and are ready to go! 


## SAS macro / DVS template 

This application will link two files on sharepoint: 





