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Merged
spgarbet merged 4 commits into from
Mar 14, 2026
Merged

Delimiter 507 #508

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b140020
Adding documentation on csv_delimiter, ability to set as argument on …
spgarbet Mar 13, 2026
6d78e30
Removing hard coded csv delimiter from exportExternalCoding #507
spgarbet Mar 13, 2026
ce27db5
Added csv_delimiter to every call I could find #507
spgarbet Mar 13, 2026
c5261ee
exportFileRepositoryListing csv_delimiter #507
spgarbet Mar 13, 2026
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2 changes: 1 addition & 1 deletion R/createFileRepositoryFolder.R
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Original file line number Diff line number Diff line change
Expand Up @@ -153,7 +153,7 @@ createFileRepositoryFolder.redcapApiConnection <- function(rcon,
rcon$flush_fileRepository()

# Prepare Output --------------------------------------------------
NewFolder <- as.data.frame(response)
NewFolder <- as.data.frame(response, sep = rcon$csv_delimiter())

NewFolder$name <- rep(name, nrow(NewFolder))

Expand Down
22 changes: 11 additions & 11 deletions R/exportArms.R
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Expand Up @@ -10,35 +10,35 @@ exportArms <- function(rcon, ...){
#' @order 4
#' @export

exportArms.redcapApiConnection <- function(rcon,
arms = character(0),
exportArms.redcapApiConnection <- function(rcon,
arms = character(0),
...)
{
if (is.numeric(arms)) arms <- as.character(arms)

# Argument Validation ---------------------------------------------
coll <- checkmate::makeAssertCollection()

checkmate::assert_class(x = rcon,
classes = "redcapApiConnection",
add = coll)

checkmate::assert_character(x = arms,
add = coll)

checkmate::reportAssertions(coll)

if(rcon$projectInformation()$is_longitudinal == 0){
return(REDCAP_ARMS_STRUCTURE) # defined in redcapDataStructure.R
}

# Build the body list ---------------------------------------------
body <- c(list(content = 'arm',
format = 'csv',
returnFormat = 'csv'),
vectorToApiBodyList(arms,
body <- c(list(content = 'arm',
format = 'csv',
returnFormat = 'csv'),
vectorToApiBodyList(arms,
parameter_name = "arms"))

# API Call --------------------------------------------------------
as.data.frame(makeApiCall(rcon, body, ...))
as.data.frame(makeApiCall(rcon, body, ...), sep = rcon$csv_delimiter())
}
40 changes: 20 additions & 20 deletions R/exportEvents.R
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Expand Up @@ -2,7 +2,7 @@
#' @order 1
#' @export

exportEvents <- function(rcon,
exportEvents <- function(rcon,
...){
UseMethod("exportEvents")
}
Expand All @@ -11,53 +11,53 @@ exportEvents <- function(rcon,
#' @order 4
#' @export

exportEvents.redcapApiConnection <- function(rcon,
arms = NULL,
exportEvents.redcapApiConnection <- function(rcon,
arms = NULL,
...)
{
if (is.character(arms)) arms <- as.numeric(arms)

##################################################################
# Argument Validation
# Argument Validation
coll <- checkmate::makeAssertCollection()

checkmate::assert_class(x = rcon,
classes = "redcapApiConnection",
add = coll)

checkmate::assert_integerish(x = arms,
null.ok = TRUE,
add = coll)

checkmate::reportAssertions(coll)

Arms <- rcon$arms()
checkmate::assert_subset(x = arms,
choices = Arms$arm_num,

checkmate::assert_subset(x = arms,
choices = Arms$arm_num,
add = coll)

checkmate::reportAssertions(coll)

##################################################################
# Return for Classical projects

if (rcon$projectInformation()$is_longitudinal == 0){
return(REDCAP_EVENT_STRUCTURE) # Defined in redcapDataStructure.R
}

##################################################################
# Make the Body List
body <- list(content = 'event',
format = 'csv',

body <- list(content = 'event',
format = 'csv',
returnFormat = 'csv')
body <- c(body,
body <- c(body,
vectorToApiBodyList(arms, "arms"))

##################################################################
# Call the API

response <- as.data.frame(makeApiCall(rcon, body, ...))
response <- as.data.frame(makeApiCall(rcon, body, ...), sep = rcon$csv_delimiter())
if(nrow(response) == 0) REDCAP_EVENT_STRUCTURE else response
}
168 changes: 84 additions & 84 deletions R/exportExternalCoding.R
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@@ -1,165 +1,165 @@
#' @name exportExternalCoding
#' @title Export Codebook Mappings for Fields with External Dependencies
#'
#' @description These methods enable `redcapAPI` to obtain a mapping of
#' codes and associated labels for fields that have external dependencies.
#' The fields include SQL fields (dependent on another project) or
#'
#' @description These methods enable `redcapAPI` to obtain a mapping of
#' codes and associated labels for fields that have external dependencies.
#' The fields include SQL fields (dependent on another project) or
#' fields that utilize the BioPortal Ontology modules.
#'
#'
#' @inheritParams common-rcon-arg
#' @inheritParams common-dot-args
#' @inheritParams common-api-args
#' @inheritParams recordsTypedMethods
#'
#' @details These methods operate by executing two API calls to export first the
#' coded values and then the labeled values of fields with external
#' dependencies. The two exports are then used to generate the code-label
#'
#' @details These methods operate by executing two API calls to export first the
#' coded values and then the labeled values of fields with external
#' dependencies. The two exports are then used to generate the code-label
#' mappings for use in casting data.
#'
#' Fields of type `sql` are dropdown fields that are populated by a SQL
#' query to another project.
#'
#' Fields of type `bioportal` are text fields that have the BioPortal
#'
#' Fields of type `sql` are dropdown fields that are populated by a SQL
#' query to another project.
#'
#' Fields of type `bioportal` are text fields that have the BioPortal
#' Ontology module enabled as the validation method.
#'
#'
#' @return
#' Returns a named list of named character vectors.
#'
#' Each element is in the list is named for the field it maps.
#'
#' The character vectors are name-value pairs where the name is the labeled
#' Returns a named list of named character vectors.
#'
#' Each element is in the list is named for the field it maps.
#'
#' The character vectors are name-value pairs where the name is the labeled
#' data and the value is the coded data.
#'
#'
#' @examples
#' \dontrun{
#' unlockREDCap(connections = c(rcon = "project_alias"),
#' url = "your_redcap_url",
#' keyring = "API_KEYs",
#' unlockREDCap(connections = c(rcon = "project_alias"),
#' url = "your_redcap_url",
#' keyring = "API_KEYs",
#' envir = globalenv())
#'
#'
#' exportExternalCoding(rcon)
#' }
#'
#'

exportExternalCoding <- function(rcon,
fields,
exportExternalCoding <- function(rcon,
fields,
...){
UseMethod("exportExternalCoding")
}

#' @rdname exportExternalCoding
#' @export

exportExternalCoding.redcapApiConnection <- function(rcon,
fields = NULL,
...,
exportExternalCoding.redcapApiConnection <- function(rcon,
fields = NULL,
...,
batch_size = 1000)
{
###################################################################
# Argument Validation ####

coll <- checkmate::makeAssertCollection()
checkmate::assert_class(x = rcon,
class = "redcapConnection",

checkmate::assert_class(x = rcon,
class = "redcapConnection",
add = coll)
checkmate::assert_character(x = fields,
null.ok = TRUE,
any.missing = FALSE,

checkmate::assert_character(x = fields,
null.ok = TRUE,
any.missing = FALSE,
add = coll)
checkmate::assert_integerish(x = batch_size,

checkmate::assert_integerish(x = batch_size,
len = 1,
lower = 1,
null.ok = TRUE,
any.missing = FALSE,
lower = 1,
null.ok = TRUE,
any.missing = FALSE,
add = coll)

checkmate::reportAssertions(coll)
checkmate::assert_subset(x = fields,
choices = rcon$metadata()$field_name,

checkmate::assert_subset(x = fields,
choices = rcon$metadata()$field_name,
add = coll)

checkmate::reportAssertions(coll)

###################################################################
# Functionality ####

MetaData <- rcon$metadata()
external_fields <-
MetaData$field_name[grepl("BIOPORTAL",
MetaData$select_choices_or_calculations,
ignore.case = TRUE) |
external_fields <-
MetaData$field_name[grepl("BIOPORTAL",
MetaData$select_choices_or_calculations,
ignore.case = TRUE) |
(!is.na(MetaData$field_type) & MetaData$field_type == "sql")]

if (is.null(fields)){
fields <- external_fields
} else {
fields <- fields[fields %in% external_fields]
}

if (length(fields) == 0){
return(list())
}
body <- c(list(content = "record",
format = "csv",
returnFormat = "csv",
type = "flat",
rawOrLabel = "raw"),

body <- c(list(content = "record",
format = "csv",
returnFormat = "csv",
type = "flat",
rawOrLabel = "raw"),
vectorToApiBodyList(fields, "fields"))

Code <-
Code <-
if (!is.null(batch_size)){
.exportRecordsTyped_Batched(rcon = rcon,
body = body,
.exportRecordsTyped_Batched(rcon = rcon,
body = body,
records = NULL,
csv_delimiter = ",",
csv_delimiter = rcon$csv_delimiter(),
batch_size = batch_size,
...)
} else {
.exportRecordsTyped_Unbatched(rcon = rcon,
body = body,
.exportRecordsTyped_Unbatched(rcon = rcon,
body = body,
records = NULL,
csv_delimiter = ",",
csv_delimiter = rcon$csv_delimiter(),
...)
}

body$rawOrLabel <- "label"
Label <-

Label <-
if (!is.null(batch_size)){
.exportRecordsTyped_Batched(rcon = rcon,
body = body,
.exportRecordsTyped_Batched(rcon = rcon,
body = body,
records = NULL,
csv_delimiter = ",",
csv_delimiter = rcon$csv_delimiter(),
batch_size = batch_size,
...)
} else {
.exportRecordsTyped_Unbatched(rcon = rcon,
body = body,
records = NULL,
csv_delimiter = ",",
.exportRecordsTyped_Unbatched(rcon = rcon,
body = body,
records = NULL,
csv_delimiter = rcon$csv_delimiter(),
...)
}

External <- vector("list", length(fields))
names(External) <- fields

for (f in fields){
ThisCode <- data.frame(code = Code[[f]],
label = Label[[f]],
ThisCode <- data.frame(code = Code[[f]],
label = Label[[f]],
stringsAsFactors = FALSE)
ThisCode <- ThisCode[!duplicated(ThisCode), ]
ThisCode <- ThisCode[!is.na(ThisCode$code), ]

mapping <- ThisCode$code
names(mapping) <- ThisCode$label

External[[f]] <- mapping
}

External
}
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