Added namespace formatting to scripts

R/utils.R

@@ -19,51 +19,51 @@
 #' @export
 
 get_env_var <- function(var_name) {
-
   # if running on server, use Sys.getenv()
   if (Sys.getenv()["USERNAME"][[1]] == "rstudio-connect") {
-
     return(Sys.getenv(var_name))
 
     # if running locally, try keyring first
   } else {
-
     # try keyring
-    kr <- try({
-      var <- keyring::key_get(var_name)
-      TRUE },
-      silent = TRUE)
+    kr <- try(
+      {
+        var <- keyring::key_get(var_name)
+        TRUE
+      },
+      silent = TRUE
+    )
 
     # if keyring worked, return
     if (kr[1] == TRUE) {
       return(var)
 
       # otherwise, try Sys.getenv
     } else {
-
-      sys_env <- try({
-        var <- Sys.getenv(var_name)
-        TRUE},
-        silent = TRUE)
+      sys_env <- try(
+        {
+          var <- Sys.getenv(var_name)
+          TRUE
+        },
+        silent = TRUE
+      )
 
       # if Sys.gentenv worked, give warning and return
       if (sys_env[1] == TRUE & var != "") {
-
-        warning(glue(
+        warning(glue::glue(
           "variable {var_name} found in Renviron file but not windows credentials. ",
           "Update your process to use keyring and not .Renviron file by doing the ",
           "following: \n",
           " 1. Run: keyring::key_set(service = '{var_name}') \n",
           " 2. Enter the variable value in the text box \n",
           " 3. Delete the variable {var_name} from your .Renviron file \n"
-        )
-        )
+        ))
 
         return(var)
 
         # otherwise, variable not found
       } else {
-        stop(glue("variable {var_name} not found using keyring or Sys.getenv()"))
+        stop(glue::glue("variable {var_name} not found using keyring or Sys.getenv()"))
       }
     }
   }

R/zzz.R

@@ -1,3 +1,3 @@
-#.onAttach <- function(libname, pkgname) {
+# .onAttach <- function(libname, pkgname) {
 #  packageStartupMessage("WARNING: This package is still in development, use at own risk.")
-#}
+# }

README.Rmd

@@ -8,7 +8,6 @@ knitr::opts_chunk$set(
   comment = "#>",
   fig.path = "tools/README-"
 )
-
 ```
 
 # SQL R Tools
@@ -69,37 +68,35 @@ again*
 To set up GitHub PAT in the Git Credential Store & install package:
 
 ```{r, install, eval=FALSE}
-
 # Install required packages
 install.packages("usethis")
 install.packages("gitcreds")
 install.packages("remotes")
 install.packages("pak")
 
 # set up GitHub PAT. Note: if a GitHub PAT has already been saved, the following
-# will give an option to replace the credentials. Run the function, select the 
-# relevant option and update the PAT with the one just copied from GitHub. 
+# will give an option to replace the credentials. Run the function, select the
+# relevant option and update the PAT with the one just copied from GitHub.
 gitcreds::gitcreds_set()
 
 # Check has been set properly, the below should return a list with details of:
-# protocol, host, username and password. None of these should be NA, the 
-# password should have "<-- hidden -->". 
+# protocol, host, username and password. None of these should be NA, the
+# password should have "<-- hidden -->".
 gitcreds::gitcreds_get()
 
 # If the above doesn't look correct:
-#  1. Make sure you don't have GITHUB_PAT set in your Renviron file. If you do, 
+#  1. Make sure you don't have GITHUB_PAT set in your Renviron file. If you do,
 #     delete it, restart R, and check it's no longer in use by running
-#     Sys.getenv("GITHUB_PAT"), this should return "". 
-#  2. Delete your GITHUB_PAT on GitHub at https://github.com/settings/tokens and 
-#     re-create the PAT using the instructions above (this may have failed if 
-#     you already had a GitHub PAT set up). 
+#     Sys.getenv("GITHUB_PAT"), this should return "".
+#  2. Delete your GITHUB_PAT on GitHub at https://github.com/settings/tokens and
+#     re-create the PAT using the instructions above (this may have failed if
+#     you already had a GitHub PAT set up).
 
-# If the output of gitcreds::gitcreds_get() still looks incorrect, contact the 
-# author of this package. 
+# If the output of gitcreds::gitcreds_get() still looks incorrect, contact the
+# author of this package.
 
 # install the package (see notes below if this fails)
 pak::pkg_install("Notts-HC/SQLRtools")
-
 ```
 
 If you have a `GITHUB_PAT` set up in the Renviron file **delete it**. The 
@@ -128,8 +125,6 @@ Sys.setenv(GITHUB_PAT = gitcreds::gitcreds_get(use_cache = FALSE)$password)
 
 # install using remotes
 remotes::install_github("Notts-HC/SQLRtools")
-
-
 ```
 
 ## About
@@ -154,7 +149,6 @@ unloadNamespace("SQLRtools")
 
 ```{r, error = TRUE}
 covr::package_coverage()
-
 ```
 
 ## Using the package
@@ -167,55 +161,57 @@ server.
 The below gives examples of connecting to a MSSQL server and MYSQL server:
 
 ```{r sql connection, eval=FALSE}
-
 library(SQLRtools)
 
 
 # set connection to MS SQL server
-ms_sql_server <- sql_server$new(driver = "SQL Server",
-                                server = get_env_var("MSSQL_SERVER"),
-                                database = get_env_var("MSSQL_DATABASE"))
+ms_sql_server <- sql_server$new(
+  driver = "SQL Server",
+  server = get_env_var("MSSQL_SERVER"),
+  database = get_env_var("MSSQL_DATABASE")
+)
 
 # set connect to MySQL server
-my_sql_server <- sql_server$new(driver = "MySQL ODBC 8.0 Unicode Driver",
-                                server = get_env_var("HOST_NAME"),
-                                database = get_env_var("MYSQL_DB"),
-                                port = get_env_var("MYSQL_PORT"),
-                                uid = get_env_var("MYSQL_USER"),
-                                pwd = get_env_var("MYSQL_PASSWORD"))
-
+my_sql_server <- sql_server$new(
+  driver = "MySQL ODBC 8.0 Unicode Driver",
+  server = get_env_var("HOST_NAME"),
+  database = get_env_var("MYSQL_DB"),
+  port = get_env_var("MYSQL_PORT"),
+  uid = get_env_var("MYSQL_USER"),
+  pwd = get_env_var("MYSQL_PASSWORD")
+)
 ```
 
 The methods listed above can now be used with these connections to:
 
 ##### Upload & query data
 
 ```{r basic sql examples, eval=FALSE}
-
 # create a basic temp table
-my_data <- data.frame(a = c("a", "b", "c"),
-                      b = 1:3)
+my_data <- data.frame(
+  a = c("a", "b", "c"),
+  b = 1:3
+)
 
 # upload as a temporary table - note that generally close_conn should be TRUE
-# (which is the default setting), but it needs to be FALSE here so the 
+# (which is the default setting), but it needs to be FALSE here so the
 # connection isn't shut after uploading the temporary table, as this would drop
-# the temporary table straight away. 
-ms_sql_server$upload(data = my_data,
-                     table_name = "#SQLRtools_example",
-                     close_conn = FALSE)
+# the temporary table straight away.
+ms_sql_server$upload(
+  data = my_data,
+  table_name = "#SQLRtools_example",
+  close_conn = FALSE
+)
 
 # get the data
-sql_data <- ms_sql_server$get("SELECT * 
+sql_data <- ms_sql_server$get("SELECT *
                                FROM #SQLRtools_example")
-
-
 ```
 
 
 ##### Explore databases & their objects
 
 ```{r details of objects on server, eval=FALSE}
-
 # get databases in server
 ms_sql_dbs <- ms_sql_server$databases()
 
@@ -226,50 +222,57 @@ my_sql_db_tables <- ms_sql_server$db_tables(database = ms_sql_dbs$name[20])
 my_sql_db_views <- ms_sql_server$db_views(database = ms_sql_dbs$name[20])
 
 # get meta data of table in given tables
-my_sql_meta_data <- ms_sql_server$meta_data(database = ms_sql_dbs$name[20],
-                                            objects = my_sql_db_views$view_name[1:5],
-                                            details = FALSE)
+my_sql_meta_data <- ms_sql_server$meta_data(
+  database = ms_sql_dbs$name[20],
+  objects = my_sql_db_views$view_name[1:5],
+  details = FALSE
+)
 
 names(my_sql_meta_data)[1]
 View(my_sql_meta_data[1][[1]])
-
 ```
 
 ##### Avoid the "Invalid Descriptor Index" issue
 
 ```{r invalid descriptor index example, eval=FALSE}
-
 # create a basic temp table
-my_data <- data.frame(a = c("a", "b", "c"),
-                      b = 1:3)
+my_data <- data.frame(
+  a = c("a", "b", "c"),
+  b = 1:3
+)
 
-# upload as a temporary table 
-ms_sql_server$upload(data = my_data,
-                     table_name = "#SQLRtools_example",
-                     close_conn = FALSE)
+# upload as a temporary table
+ms_sql_server$upload(
+  data = my_data,
+  table_name = "#SQLRtools_example",
+  close_conn = FALSE
+)
 
 # change the data type of column a to varchar(max)
 ms_sql_server$run("ALTER TABLE #SQLRtools_example
                    ALTER COLUMN a varchar(max);",
-                  close_conn = FALSE)
+  close_conn = FALSE
+)
 
 # try extracting the data
 ms_sql_server$get("SELECT * FROM #SQLRtools_example",
-                  close_conn = FALSE)
+  close_conn = FALSE
+)
 
 # use method order_object_fields to avoid issue
 
 # get all the fields ordered by data type
-table_fields <- ms_sql_server$order_object_fields(object = "#SQLRtools_example",
-                                                  close_conn = FALSE)
+table_fields <- ms_sql_server$order_object_fields(
+  object = "#SQLRtools_example",
+  close_conn = FALSE
+)
 
 # now extract all the data
-ms_sql_server$get(glue("SELECT {table_fields} 
+ms_sql_server$get(glue("SELECT {table_fields}
                         FROM #SQLRtools_example"))
 
-# note that the above table only has 2 fields. Where your trying to run 
-# select * on a table with a lot of fields and multiple varchar(max) or 
-# geometry feilds, the above makes life a lot easier (notwithstanding the fact 
-# it's good practice to avoid 'select *' in SQL where possible). 
-
+# note that the above table only has 2 fields. Where your trying to run
+# select * on a table with a lot of fields and multiple varchar(max) or
+# geometry feilds, the above makes life a lot easier (notwithstanding the fact
+# it's good practice to avoid 'select *' in SQL where possible).
 ```

SQLRtools.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: db9d44e7-f57d-4157-a5ba-a48925b20d99
 
 RestoreWorkspace: Default
 SaveWorkspace: Default