csvdelimiter and project csv delimiter not consistently respected in exports and imports

DESCRIPTION

@@ -24,7 +24,8 @@ Authors@R: c(
     person("Philip", "Chase", role="ctb"),
     person("Paddy", "Tobias", role = "ctb"),
     person("Michael", "Chirico", role = "ctb"),
-    person("William", "Sharp", role="ctb"))
+    person("William", "Sharp", role="ctb"),
+    person("Alexander", "Strübing", role="ctb"))
 Maintainer: Shawn Garbett <shawn.garbett@vumc.org>
 Description: Access data stored in 'REDCap' databases using the Application
     Programming Interface (API).  'REDCap' (Research Electronic Data CAPture;

R/docsRecordsTypedMethods.R

@@ -42,7 +42,7 @@
 #'   Otherwise, records created or modified after this date will be returned.
 #' @param date_end `POSIXct(1)` or `NULL`. Ignored if `NULL` (default). 
 #'   Otherwise, records created or modified before this date will be returned.
-#' @param csv_delimiter `character`. One of `c(",", "\t", ";", "|", "^")`. Designates the
+#' @param csv_delimiter `character`. One of `c(",", ";", "\t", " ", "|", "^")`. Designates the
 #'   delimiter for the CSV file received from the API.
 #' @param batch_size `integerish(1)` or `NULL`. When `NULL`,
 #'   all records are pulled. Otherwise, the records all pulled in batches of this size.

R/exportDags.R

@@ -11,28 +11,29 @@ exportDags <- function(rcon, ...){
 #' @order 4
 #' @export
 
-exportDags.redcapApiConnection <- function(rcon, 
+exportDags.redcapApiConnection <- function(rcon,
                                            ...)
 {
   ###################################################################
   # Argument Validation                                          ####
-  
+
   coll <- checkmate::makeAssertCollection()
-  
-  checkmate::assert_class(x = rcon, 
-                          classes = "redcapApiConnection", 
+
+  checkmate::assert_class(x = rcon,
+                          classes = "redcapApiConnection",
                           add = coll)
 
   checkmate::reportAssertions(coll)
-  
+
   ###################################################################
   # Make the API Body list                                       ####
-
-  body <- list(content = "dag", 
-               format = "csv", 
-               returnFormat = "csv")
+
+  body <- list(content = "dag",
+               format = "csv",
+               returnFormat = "csv",
+               csvDelimiter = rcon$csv_delimiter())
 
   ###################################################################
   # Call the API                                                 ####
-  as.data.frame(makeApiCall(rcon, body, ...))
+  as.data.frame(makeApiCall(rcon, body, ...), sep = rcon$csv_delimiter())
 }

R/exportFieldNames.R

@@ -135,5 +135,6 @@ exportFieldNames.redcapApiConnection <- function(rcon,
   # Make the API Call -----------------------------------------------
   read.csv(text = as.character(makeApiCall(rcon, body, ...)), 
            na.strings = "", 
-           stringsAsFactors = FALSE)
+           stringsAsFactors = FALSE,
+           sep = rcon$csv_delimiter())
 }

R/exportProjectInformation.R

@@ -30,9 +30,10 @@ exportProjectInformation.redcapApiConnection <- function(rcon,
 
   body <- list(content = 'project',
                format = 'csv',
-               returnFormat = 'csv')
+               returnFormat = 'csv',
+               csvDelimiter = rcon$csv_delimiter())
 
    ##################################################################
   # Call the API
-  as.data.frame(makeApiCall(rcon, body, ...))
+  as.data.frame(makeApiCall(rcon, body, ...), sep = rcon$csv_delimiter())
 }

R/exportRecordsTyped.R

@@ -47,7 +47,7 @@ exportRecordsTyped.redcapApiConnection <-
     filter_empty_rows = TRUE,
     warn_zero_coded = TRUE,
     ...,
-    csv_delimiter  = ",",
+    csv_delimiter  = rcon$csv_delimiter(),
     batch_size     = 100L)
 {
   logEvent("INFO", call='exportRecordsTyped',
@@ -112,7 +112,7 @@ exportRecordsTyped.redcapApiConnection <-
                                add = coll)
 
   csv_delimiter <- checkmate::matchArg(x         = csv_delimiter,
-                                       choices   = c(",", "\t", ";", "|", "^"),
+                                       choices   = c(",", ";", "\t", " ", "|", "^"),
                                        .var.name = "csv_delimiter",
                                        add = coll)
 
@@ -682,7 +682,8 @@ exportRecordsTyped.redcapOfflineConnection <- function(rcon,
     record_response <- makeApiCall(rcon,
                                    body = c(list(content = "record",
                                                  format = "csv",
-                                                 outputFormat = "csv"),
+                                                 outputFormat = "csv",
+                                                 csvDelimiter = rcon$csv_delimiter()),
                                             vectorToApiBodyList(target_field,
                                                                 "fields")),
                                    log=FALSE,

R/exportReportsTyped.R

@@ -59,7 +59,7 @@ exportReportsTyped.redcapApiConnection <- function(rcon,
                          add = coll)
 
   csv_delimiter <- checkmate::matchArg(x = csv_delimiter, 
-                                       choices = c(",", "\t", ";", "|", "^"),
+                                       choices = c(",", ";", "\t", " ", "|", "^"),
                                        .var.name = "csv_delimiter",
                                        add = coll)
 

R/importDags.R

@@ -53,7 +53,7 @@ importDags.redcapApiConnection <- function(rcon,
                action = "import", 
                format = "csv", 
                returnFormat = "csv", 
-               data = writeDataForImport(data))
+               data = writeDataForImport(data, csv_delimiter = rcon$csv_delimiter()))
 
   ###################################################################
   # Call the API                                                 ####

R/redcapConnection.R

@@ -236,6 +236,9 @@ redcapConnection <- function(url = getOption('redcap_api_url'),
                   length.out = rtry)
   rtry_q <- retry_quietly
 
+  # CSV delimiter state for this connection -------------------------
+  csv_delim <- ","
+
   getter <- function(export, ...){
     switch(export,
            "metadata" = exportMetaData(rc),
@@ -397,9 +400,20 @@ redcapConnection <- function(url = getOption('redcap_api_url'),
                                   len = 1,
                                   any.missing = FALSE)
         rtry_q <<- rq
-      }
+      },
+
+      set_csv_delimiter = function(d) {
+      	checkmate::assert_choice(
+      		x = d,
+      		choices = c(",", ";", "\t", " ", "|", "^")
+      	)
+      	csv_delim <<- d
+      },
+      csv_delimiter = function() csv_delim
     )
   class(rc) <- c("redcapApiConnection", "redcapConnection")
+  # Initialize csv_delimiter with default
+  rc$set_csv_delimiter(",")
   rc
 }
 

R/writeDataForImport.R

@@ -5,9 +5,11 @@
 #'   of a CSV for import through the API.
 #'   
 #' @param data `data.frame` to be imported to the API
-#' 
+#' @param csv_delimiter `character(1)` Delimiter used to separate fields in the generated CSV
+#'   string. Defaults to `","`.
+#'
 
-writeDataForImport <- function(data){
+writeDataForImport <- function(data, csv_delimiter = ","){
   coll <- checkmate::makeAssertCollection()
 
   checkmate::assert_data_frame(x = data, 
@@ -17,10 +19,13 @@ writeDataForImport <- function(data){
 
   output <- 
     utils::capture.output(
-      utils::write.csv(data,
-                       file = "",
-                       na = "",
-                       row.names = FALSE)
+      utils::write.table(data,
+                         file = "",
+                         sep = csv_delimiter,
+                         na = "",
+                         row.names = FALSE,
+                         col.names = TRUE,
+                         qmethod = "double")
     )
 
   paste0(output, collapse = "\n")