checkmate parameters

ref #190
OuhscBbmc · May 31, 2018 · 1686b2e · 1686b2e
1 parent c8bf54d
commit 1686b2e
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Showing 3 changed files with 23 additions and 2 deletions.
diff --git a/R/project-simple.R b/R/project-simple.R
@@ -1,5 +1,7 @@
 
 populate_project_simple <- function( batch = FALSE ) {
+  checkmate::assert_logical(batch, any.missing=F, len=1)
+
   if( !requireNamespace("testthat") ) stop("The function REDCapR:::populate_project_simple() cannot run if the `testthat` package is not installed.  Please install it and try again.")
 
   #Declare the server & user information
@@ -30,7 +32,7 @@ populate_project_simple <- function( batch = FALSE ) {
   #Import the data into the REDCap project
   testthat::expect_message(
     returned_object <- if( batch ) {
-      REDCapR::redcap_write(ds=dsToWrite, redcap_uri=uri, token=token, verbose=TRUE)
+      REDCapR::redcap_write(        ds=dsToWrite, redcap_uri=uri, token=token, verbose=TRUE)
     } else {
       REDCapR::redcap_write_oneshot(ds=dsToWrite, redcap_uri=uri, token=token, verbose=TRUE)
     }
@@ -62,6 +64,9 @@ clear_project_simple <- function( verbose = TRUE ) {
 }
 
 clean_start_simple <- function( batch = FALSE, delay_in_seconds = 1 ) {
+  checkmate::assert_logical( batch            , any.missing=F, len=1)
+  checkmate::assert_numeric( delay_in_seconds , any.missing=F, len=1, lower=0)
+
   if( !requireNamespace("testthat") ) stop("The function REDCapR:::populate_project_simple() cannot run if the `testthat` package is not installed.  Please install it and try again.")
   testthat::expect_message(
     clear_result <- clear_project_simple(),
@@ -81,6 +86,9 @@ clean_start_simple <- function( batch = FALSE, delay_in_seconds = 1 ) {
 }
 
 upload_file_simple <- function( redcap_uri, token=token ) {
+  checkmate::assert_character(redcap_uri, any.missing=F, len=1, min.chars = 5)
+  checkmate::assert_character(token     , any.missing=F, len=1, pattern="^\\w{32}$")
+
   records <- 1:5
   file_paths <- base::file.path(pkgload::inst(name="REDCapR"), paste0("test-data/mugshot-", records, ".jpg"))
 

diff --git a/R/redcap-column-sanitize.R b/R/redcap-column-sanitize.R
@@ -36,6 +36,11 @@ redcap_column_sanitize <- function(
   encoding_initial        = "latin1",
   substitution_character  = "?" ) {
 
+  checkmate::assert_data_frame(d                      , any.missing=F)
+  checkmate::assert_character( column_names           , any.missing=F)
+  checkmate::assert_character( encoding_initial       , any.missing=F, len=1)
+  checkmate::assert_character( substitution_character , any.missing=F, len=1, pattern="^.$")
+
   for( column in column_names ) {
     d[[column]] <- base::iconv(
       x     = d[[column]],

diff --git a/R/validate.R b/R/validate.R
@@ -41,8 +41,10 @@
 #' )
 #' validate_for_write(d = d)
 
-
 validate_no_logical <- function( data_types, stop_on_error=FALSE ) {
+  checkmate::assert_character(data_types, any.missing=F, min.len=1, min.chars=2)
+  checkmate::assert_logical(stop_on_error, any.missing=F, len=1)
+
   # indices <- which(sapply(d, class)=="logical")
   indices <- which(data_types=="logical")
 
@@ -64,7 +66,11 @@ validate_no_logical <- function( data_types, stop_on_error=FALSE ) {
     )
   }
 }
+
 validate_field_names <- function( field_names, stop_on_error=FALSE ) {
+  checkmate::assert_character(field_names, any.missing=F, null.ok=T, min.len=1, min.chars=2)
+  checkmate::assert_logical(stop_on_error, any.missing=F, len=1)
+
   pattern <- "^[0-9a-z_]+$"
 
   indices <- which(!grepl(pattern, x=field_names, perl=TRUE))
@@ -88,6 +94,8 @@ validate_field_names <- function( field_names, stop_on_error=FALSE ) {
 }
 
 validate_for_write <- function( d ) {
+  checkmate::assert_data_frame(d, any.missing=F)
+
   lst_concerns <- list(
     validate_no_logical(sapply(d, class)),
     validate_field_names(colnames(d))