tidy

ref #213
OuhscBbmc · May 29, 2018 · 45e53bc · 45e53bc
1 parent a3c1bf2
commit 45e53bc
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Showing 3 changed files with 18 additions and 65 deletions.
diff --git a/R/redcap-metadata-read.R b/R/redcap-metadata-read.R
@@ -46,13 +46,15 @@
 #' }
 
 redcap_metadata_read <- function(
-  redcap_uri, token, forms=NULL, forms_collapsed="",
-  fields=NULL, fields_collapsed="",
-  verbose=TRUE, config_options=NULL
+  redcap_uri,
+  token,
+  forms             = NULL, forms_collapsed  = "",
+  fields            = NULL, fields_collapsed = "",
+  verbose           = TRUE,
+  config_options    = NULL
 ) {
   #TODO: NULL verbose parameter pulls from getOption("verbose")
 
-  # start_time <- Sys.time()
   checkmate::assert_character(redcap_uri                , any.missing=F, len=1, pattern="^.{1,}$")
   checkmate::assert_character(token                     , any.missing=F, len=1, pattern="^.{1,}$")
 
@@ -69,18 +71,8 @@ redcap_metadata_read <- function(
     fields   = fields_collapsed
   )
 
+  # This is the important line that communicates with the REDCap server.
   kernel <- kernel_api(redcap_uri, post_body, config_options)
-  # result <- httr::POST(
-  #   url      = redcap_uri,
-  #   body     = post_body,
-  #   config   = config_options
-  # )
-  #
-  # status_code     <- result$status
-  # success         <- (status_code==200L)
-  # raw_text        <- httr::content(result, "text")
-  # # TODO: convert all line endings to "\n"
-  # elapsed_seconds <- as.numeric(difftime(Sys.time(), start_time, units="secs"))
 
   if( kernel$success ) {
     col_types <- readr::cols(field_name = readr::col_character(), .default = readr::col_character())
@@ -99,17 +91,15 @@ redcap_metadata_read <- function(
         kernel$status_code, "."
       )
 
-      # If an operation is successful, the `raw_text` is no longer returned to save RAM.  The content is not really necessary with httr's status message exposed.
-      kernel$raw_text <- ""
+      kernel$raw_text   <- "" # If an operation is successful, the `raw_text` is no longer returned to save RAM.  The content is not really necessary with httr's status message exposed.
     } else {
-      success <- FALSE #Override the 'success' determination from the http status code.
-      ds <- data.frame() #Return an empty data.frame
-      outcome_message <- paste0("The REDCap metadata export failed.  The http status code was ", kernel$status_code, ".  The 'raw_text' returned was '", kernel$raw_text, "'.")
+      success           <- FALSE #Override the 'success' determination from the http status code.
+      ds                <- data.frame() #Return an empty data.frame
+      outcome_message   <- paste0("The REDCap metadata export failed.  The http status code was ", kernel$status_code, ".  The 'raw_text' returned was '", kernel$raw_text, "'.")
     }
-  }
-  else {
-    ds <- data.frame() #Return an empty data.frame
-    outcome_message <- paste0("The REDCapR metadata export operation was not successful.  The error message was:\n",  kernel$raw_text)
+  } else {
+    ds                  <- data.frame() #Return an empty data.frame
+    outcome_message     <- paste0("The REDCapR metadata export operation was not successful.  The error message was:\n",  kernel$raw_text)
   }
 
   if( verbose )

diff --git a/R/redcap-read-oneshot-eav.R b/R/redcap-read-oneshot-eav.R
@@ -108,8 +108,6 @@ redcap_read_oneshot_eav <- function(
 ) {
   #TODO: NULL verbose parameter pulls from getOption("verbose")
 
-  # start_time <- Sys.time()
-
   checkmate::assert_character(redcap_uri                , any.missing=F, len=1, pattern="^.{1,}$")
   checkmate::assert_character(token                     , any.missing=F, len=1, pattern="^.{1,}$")
   checkmate::assert_atomic(records                      , any.missing=T, min.len=0)
@@ -169,25 +167,7 @@ redcap_read_oneshot_eav <- function(
   if( nchar(events_collapsed ) > 0 ) post_body$events   <- events_collapsed
 
   # This is the important line that communicates with the REDCap server.
-  kernel <- kernel_api(redcap_uri, post_body, config_options)
-
-  # result <- httr::POST(
-  #   url     = redcap_uri,
-  #   body    = post_body,
-  #   config  = config_options
-  # )
-  #
-  # status_code           <- result$status
-  # success               <- (status_code==200L)
-  # raw_text              <- httr::content(result, "text")
-  # raw_text              <- gsub("\r\n", "\n", raw_text)
-  # elapsed_seconds       <- as.numeric(difftime(Sys.time(), start_time, units="secs"))
-  #
-  # # raw_text <- "The hostname (redcap-db.hsc.net.ou.edu) / username (redcapsql) / password (XXXXXX) combination could not connect to the MySQL server. \r\n\t\tPlease check their values."
-  # regex_cannot_connect  <- "^The hostname \\((.+)\\) / username \\((.+)\\) / password \\((.+)\\) combination could not connect.+"
-  # regex_empty           <- "^\\s+$"
-  #
-  # success     <- (success & !any(grepl(regex_cannot_connect, raw_text)) & !any(grepl(regex_empty, raw_text)))
+  kernel      <- kernel_api(redcap_uri, post_body, config_options)
 
   ds_metadata <- REDCapR::redcap_metadata_read(redcap_uri, token, forms_collapsed=forms_collapsed)$data
   ds_variable <- REDCapR::redcap_variables(redcap_uri, token)$data
@@ -271,8 +251,7 @@ redcap_read_oneshot_eav <- function(
         round(kernel$elapsed_seconds, 1), " seconds.  The http status code was ", kernel$status_code, "."
       )
 
-      # If an operation is successful, the `raw_text` is no longer returned to save RAM.  The content is not really necessary with httr's status message exposed.
-      kernel$raw_text <- ""
+      kernel$raw_text   <- "" # If an operation is successful, the `raw_text` is no longer returned to save RAM.  The content is not really necessary with httr's status message exposed.
     } else {
       success           <- FALSE #Override the 'success' determination from the http status code.
       ds_2              <- tibble::tibble() #Return an empty data.frame

diff --git a/R/redcap-read-oneshot.R b/R/redcap-read-oneshot.R
@@ -155,24 +155,8 @@ redcap_read_oneshot <- function(
   if( nchar(forms_collapsed  ) > 0 ) post_body$forms    <- forms_collapsed
   if( nchar(events_collapsed ) > 0 ) post_body$events   <- events_collapsed
 
+  # This is the important line that communicates with the REDCap server.
   kernel <- kernel_api(redcap_uri, post_body, config_options)
-  # result <- httr::POST(
-  #   url     = redcap_uri,
-  #   body    = post_body,
-  #   config  = config_options
-  # )
-
-  # status_code           <- result$status
-  # success               <- (status_code==200L)
-  # raw_text              <- httr::content(result, "text")
-  # raw_text              <- gsub("\r\n", "\n", raw_text) # Convert all line-ending to linux-style
-  # elapsed_seconds       <- as.numeric(difftime(Sys.time(), start_time, units="secs"))
-  #
-  # # raw_text <- "The hostname (redcap-db.hsc.net.ou.edu) / username (redcapsql) / password (XXXXXX) combination could not connect to the MySQL server. \r\n\t\tPlease check their values."
-  # regex_cannot_connect  <- "^The hostname \\((.+)\\) / username \\((.+)\\) / password \\((.+)\\) combination could not connect.+"
-  # regex_empty           <- "^\\s+$"
-  #
-  # success     <- (success & !any(grepl(regex_cannot_connect, raw_text)) & !any(grepl(regex_empty, raw_text)))
 
   if( kernel$success ) {
     col_types <- if( guess_type ) NULL else readr::cols(.default=readr::col_character())
@@ -211,7 +195,7 @@ redcap_read_oneshot <- function(
       #
       # ds <- base::as.data.frame(ds)
 
-      kernel$raw_text <- "" # If an operation is successful, the `raw_text` is no longer returned to save RAM.  The content is not really necessary with httr's status message exposed.
+      kernel$raw_text   <- "" # If an operation is successful, the `raw_text` is no longer returned to save RAM.  The content is not really necessary with httr's status message exposed.
     } else {
       kernel$success   <- FALSE #Override the 'success' determination from the http status code.
       ds               <- data.frame() #Return an empty data.frame