Exposes config options in write operations. Partially addresses #58.

DESCRIPTION

@@ -6,7 +6,7 @@ Description: Encapsulates functions to streamline calls from R to the REDCap
     University.  The Application Programming Interface (API) offers an avenue
     to access and modify data programmatically, improving the capacity for
     literate and reproducible programming.
-Version: 0.5-18
+Version: 0.5-19
 Date: 2014-10-07
 Authors@R: c(person("Will", "Beasley", role = c("aut", "cre"), email =
     "[email protected]"), person("David", "Bard", role = "ctb"),

R/redcap_project.R

@@ -86,15 +86,15 @@ redcap_project <- setRefClass(
     write = function( 
       ds_to_write,
       batch_size = 100L, interbatch_delay = 0,
-      verbose = TRUE, cert_location = NULL) {
+      verbose = TRUE, config_options = NULL) {
 
       "Imports records to a REDCap project."
 
       return( REDCapR::redcap_write(
         ds_to_write = ds_to_write,
         batch_size = batch_size, interbatch_delay = interbatch_delay,
         redcap_uri = redcap_uri, token = token, 
-        verbose = verbose, cert_location=cert_location 
+        config_options = config_options 
       ))      
     }
 

R/redcap_read.R

@@ -20,7 +20,7 @@
 #' @param export_data_access_groups A boolean value that specifies whether or not to export the ``redcap_data_access_group'' field when data access groups are utilized in the project. Default is \code{FALSE}. See the details below.
 #' @param raw_or_label A string (either \code{'raw'} or \code{'label'} that specifies whether to export the raw coded values or the labels for the options of multiple choice fields.  Default is \code{'raw'}.
 #' @param verbose A boolean value indicating if \code{message}s should be printed to the R console during the operation.  The verbose output might contain sensitive information (\emph{e.g.} PHI), so turn this off if the output might be visible somewhere public. Optional.
-#' @param config_options  A list of options to pass to \code{POST} method in the \code{httr} package.  See the details below. Optional.
+#' @param config_options  A list of options to pass to \code{POST} method in the \code{httr} package.  See the details in \code{redcap_read_oneshot()} Optional.
 #' @param id_position  The column position of the variable that unique identifies the subject.  This defaults to the first variable in the dataset.
 #' 
 #' @return Currently, a list is returned with the following elements,

R/redcap_read_oneshot.R

@@ -121,18 +121,14 @@ redcap_read_oneshot <- function( redcap_uri, token, records=NULL, records_collap
 
   if( missing( config_options ) | is.null(config_options) ) {
     cert_location <- system.file("ssl_certs/mozilla_ca_root.crt", package="REDCapR")
+
+    if( !base::file.exists(cert_location) )
+      stop(paste0("The file specified by `cert_location`, (", cert_location, ") could not be found."))
+
     config_options <- list(cainfo=cert_location)
   }
-  #     #cert_location <- system.file("cacert.pem", package="httr")
-  #     cert_location <- system.file("ssl_certs/mozilla_ca_root.crt", package="REDCapR")
-  #     # curl_options <- RCurl::curlOptions(ssl.verifypeer=FALSE)
-
-  if( !base::file.exists(cert_location) )
-      stop(paste0("The file specified by `cert_location`, (", cert_location, ") could not be found."))
-
+
   #curl_options <- RCurl::curlOptions(cainfo=cert_location, sslversion=3)
-  # config_options <- list(cainfo=cert_location, sslversion=sslversion)
-
   # raw_text <- RCurl::postForm(
   #   uri = redcap_uri
   #   , token = token

R/redcap_write.R

@@ -13,8 +13,7 @@
 #' @param redcap_uri The URI (uniform resource identifier) of the REDCap project.  Required.
 #' @param token The user-specific string that serves as the password for a project.  Required.
 #' @param verbose A boolean value indicating if \code{message}s should be printed to the R console during the operation.  The verbose output might contain sensitive information (\emph{e.g.} PHI), so turn this off if the output might be visible somewhere public. Optional.
-#' @param cert_location  If present, this string should point to the location of the cert files required for SSL verification.  If the value is missing or NULL, the server's identity will be verified using a recent CA bundle from the \href{http://curl.haxx.se}{cURL website}.  See the details below. Optional.
-#' @param sslversion The SSL version for curl. The default is 3. Set to NULL if your server has disabled SSL v3.
+#' @param config_options  A list of options to pass to \code{POST} method in the \code{httr} package.  See the details in \code{redcap_read_oneshot()} Optional.
 #' 
 #' @return Currently, a list is returned with the following elements,
 #' \enumerate{
@@ -75,8 +74,7 @@ redcap_write <- function( ds_to_write,
                           continue_on_error = FALSE,
                           redcap_uri,
                           token,
-                          verbose = TRUE, cert_location=NULL, 
-                          sslversion = 3) {  
+                          verbose = TRUE, config_options = NULL) {  
 
   if( base::missing(redcap_uri) )
     base::stop("The required parameter `redcap_uri` was missing from the call to `redcap_write()`.")
@@ -105,8 +103,7 @@ redcap_write <- function( ds_to_write,
                                                   redcap_uri = redcap_uri,
                                                   token = token,
                                                   verbose = verbose, 
-                                                  cert_location=cert_location,
-                                                  sslversion=sslversion)
+                                                  config_options = config_options)
 
     lst_status_code[[i]] <- write_result$status_code
     # lst_status_message[[i]] <- write_result$status_message

R/redcap_write_oneshot.R

@@ -10,8 +10,7 @@
 #' @param redcap_uri The URI (uniform resource identifier) of the REDCap project.  Required.
 #' @param token The user-specific string that serves as the password for a project.  Required.
 #' @param verbose A boolean value indicating if \code{message}s should be printed to the R console during the operation.  The verbose output might contain sensitive information (\emph{e.g.} PHI), so turn this off if the output might be visible somewhere public. Optional.
-#' @param cert_location  If present, this string should point to the location of the cert files required for SSL verification.  If the value is missing or NULL, the server's identity will be verified using a recent CA bundle from the \href{http://curl.haxx.se}{cURL website}.  See the details below. Optional.
-#' @param sslversion The SSL version for curl. The default is 3. Set to NULL if your server has disabled SSL v3.
+#' @param config_options  A list of options to pass to \code{POST} method in the \code{httr} package.  See the details in \code{redcap_read_oneshot()} Optional.
 #' 
 #' @return Currently, a list is returned with the following elements,
 #' \enumerate{
@@ -69,7 +68,7 @@
 #' }
 #' 
 
-redcap_write_oneshot <- function( ds, redcap_uri, token, verbose=TRUE, cert_location=NULL, sslversion=3 ) {
+redcap_write_oneshot <- function( ds, redcap_uri, token, verbose=TRUE, config_options=NULL ) {
   #TODO: automatically convert boolean/logical class to integer/bit class
   start_time <- Sys.time()
   csvElements <- NULL #This prevents the R CHECK NOTE: 'No visible binding for global variable Note in R CMD check';  Also see  if( getRversion() >= "2.15.1" )    utils::globalVariables(names=c("csvElements")) #http://stackoverflow.com/questions/8096313/no-visible-binding-for-global-variable-note-in-r-cmd-check; http://stackoverflow.com/questions/9439256/how-can-i-handle-r-cmd-check-no-visible-binding-for-global-variable-notes-when
@@ -80,13 +79,14 @@ redcap_write_oneshot <- function( ds, redcap_uri, token, verbose=TRUE, cert_loca
   if( missing(token) )
     stop("The required parameter `token` was missing from the call to `redcap_write_oneshot()`.")     
 
-  if( missing( cert_location ) | is.null(cert_location) ) 
+  if( missing( config_options ) | is.null(config_options) ) {
     cert_location <- system.file("ssl_certs/mozilla_ca_root.crt", package="REDCapR")
-
-  if( !base::file.exists(cert_location) )
-    stop(paste0("The file specified by `cert_location`, (", cert_location, ") could not be found."))
-
-  config_options <- list(cainfo=cert_location, sslversion=sslversion)
+
+    if( !base::file.exists(cert_location) )
+      stop(paste0("The file specified by `cert_location`, (", cert_location, ") could not be found."))
+
+    config_options <- list(cainfo=cert_location)
+  }
 
   con <-  base::textConnection(object='csvElements', open='w', local=TRUE)
   write.csv(ds, con, row.names = FALSE, na="")  

man/redcap_project.Rd

@@ -26,7 +26,7 @@ functionality
   config_options = NULL)}}{Exports records from a REDCap project.}
 
 \item{\code{write(ds_to_write, batch_size = 100L, interbatch_delay = 0,
-  verbose = TRUE, cert_location = NULL)}}{Imports records to a REDCap project.}
+  verbose = TRUE, config_options = NULL)}}{Imports records to a REDCap project.}
 }}
 \examples{
 library(REDCapR) #Load the package into the current R session.

man/redcap_read.Rd

@@ -60,7 +60,7 @@ redcap_read(batch_size = 100L, interbatch_delay = 0.5,
 
   \item{config_options}{A list of options to pass to
   \code{POST} method in the \code{httr} package.  See the
-  details below. Optional.}
+  details in \code{redcap_read_oneshot()} Optional.}
 
   \item{id_position}{The column position of the variable
   that unique identifies the subject.  This defaults to the

man/redcap_write.Rd

@@ -5,7 +5,7 @@
 \usage{
 redcap_write(ds_to_write, batch_size = 100L, interbatch_delay = 0.5,
   continue_on_error = FALSE, redcap_uri, token, verbose = TRUE,
-  cert_location = NULL, sslversion = 3)
+  config_options = NULL)
 }
 \arguments{
   \item{ds_to_write}{The \code{data.frame} to be imported
@@ -36,15 +36,9 @@ redcap_write(ds_to_write, batch_size = 100L, interbatch_delay = 0.5,
   if the output might be visible somewhere public.
   Optional.}
 
-  \item{cert_location}{If present, this string should point
-  to the location of the cert files required for SSL
-  verification.  If the value is missing or NULL, the
-  server's identity will be verified using a recent CA
-  bundle from the \href{http://curl.haxx.se}{cURL website}.
-  See the details below. Optional.}
-
-  \item{sslversion}{The SSL version for curl. The default
-  is 3. Set to NULL if your server has disabled SSL v3.}
+  \item{config_options}{A list of options to pass to
+  \code{POST} method in the \code{httr} package.  See the
+  details in \code{redcap_read_oneshot()} Optional.}
 }
 \value{
 Currently, a list is returned with the following elements,

man/redcap_write_oneshot.Rd

@@ -4,7 +4,7 @@
 \title{Write/Import records to a REDCap project.}
 \usage{
 redcap_write_oneshot(ds, redcap_uri, token, verbose = TRUE,
-  cert_location = NULL, sslversion = 3)
+  config_options = NULL)
 }
 \arguments{
   \item{ds}{The \code{data.frame} to be imported into the
@@ -23,15 +23,9 @@ redcap_write_oneshot(ds, redcap_uri, token, verbose = TRUE,
   if the output might be visible somewhere public.
   Optional.}
 
-  \item{cert_location}{If present, this string should point
-  to the location of the cert files required for SSL
-  verification.  If the value is missing or NULL, the
-  server's identity will be verified using a recent CA
-  bundle from the \href{http://curl.haxx.se}{cURL website}.
-  See the details below. Optional.}
-
-  \item{sslversion}{The SSL version for curl. The default
-  is 3. Set to NULL if your server has disabled SSL v3.}
+  \item{config_options}{A list of options to pass to
+  \code{POST} method in the \code{httr} package.  See the
+  details in \code{redcap_read_oneshot()} Optional.}
 }
 \value{
 Currently, a list is returned with the following elements,