Commit ⋅ OuhscBbmc/REDCapR

      filter_logic                  = "",

      guess_type                    = TRUE,
      guess_max                     = 1000L,
      guess_max                     = 1000,
      verbose                       = TRUE,
      config_options                = NULL
    ) {

@@ -34,7 +34,6 @@

#' unsuccessful operation, it should contain diagnostic information.
#' * `elapsed_seconds`: The duration of the function.
#'
#'
#' @author Jonathan M. Mang
#' @references The official documentation can be found on the 'API Help Page'
#' and 'API Examples' pages on the REDCap wiki (*i.e.*,

@@ -110,25 +109,6 @@

        kernel$status_code
      )

      # ds <- dplyr::mutate_if(
      #   ds,
      #   is.character,
      #   function(x) dplyr::coalesce(x, "") #Replace NAs with blanks
      # )
      #
      # ds <- dplyr::mutate_if(
      #   ds,
      #   is.character,
      #   function( x ) gsub("\r\n", "\n", x, perl=TRUE)
      # )
      # ds <- dplyr::mutate_if(
      #   ds,
      #   function( x) inherits(x, "Date"),
      #   as.character
      # )
      #
      # ds <- base::as.data.frame(ds)

      # 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.

@@ -28,7 +28,8 @@

#' @param guess_type A boolean value indicating if all columns should be
#' returned as character.  If false, [readr::read_csv()] guesses the intended
#' data type for each column.  Ignored if `col_types` is not null.
#' @param guess_max A positive integer passed to [readr::read_csv()] that
#' @param guess_max A positive [base::numeric] value
#' passed to [readr::read_csv()] that
#' specifies the maximum number of records to use for guessing column types.
#' @param verbose A boolean value indicating if `message`s should be printed
#' to the R console during the operation.  The verbose output might contain

@@ -127,7 +128,7 @@


  col_types                     = NULL,
  guess_type                    = TRUE,
  guess_max                     = 1000L,
  guess_max                     = 1000,
  verbose                       = TRUE,
  config_options                = NULL
) {

@@ -142,7 +143,7 @@

  checkmate::assert_logical(  export_checkbox_label     , any.missing=FALSE, len=1)

  checkmate::assert_logical(  guess_type                , any.missing=FALSE, len=1)
  checkmate::assert_integerish(guess_max                , any.missing=FALSE, len=1, lower=1)
  checkmate::assert_numeric(   guess_max                , any.missing=FALSE, len=1, lower=1)
  checkmate::assert_logical(  verbose                   , any.missing=FALSE, len=1, null.ok=TRUE)
  checkmate::assert_list(     config_options            , any.missing=TRUE ,        null.ok=TRUE)


@@ -193,7 +193,7 @@

  checkmate::assert_logical( blank_for_gray_form_status , any.missing=FALSE, len=1)

  # placeholder: checkmate::assert_logical(  guess_type                , any.missing=FALSE, len=1)
  # placeholder: checkmate::assert_integerish(guess_max                , any.missing=FALSE, len=1, lower=1)
  # placeholder: checkmate::assert_numeric(  guess_max                , any.missing=FALSE, len=1, lower=1)
  checkmate::assert_logical(  verbose                   , any.missing=FALSE, len=1, null.ok=TRUE)
  checkmate::assert_list(     config_options            , any.missing=TRUE ,        null.ok=TRUE)


@@ -70,7 +70,8 @@

#' @param guess_type A boolean value indicating if all columns should be
#' returned as character.  If false, [readr::read_csv()] guesses the intended
#' data type for each column.  Ignored if `col_types` is not null.
#' @param guess_max A positive integer passed to [readr::read_csv()] that
#' @param guess_max A positive [base::numeric] value
#' passed to [readr::read_csv()] that
#' specifies the maximum number of records to use for guessing column types.
#' @param http_response_encoding  The encoding value passed to
#' [httr::content()].  Defaults to 'UTF-8'.

@@ -192,7 +193,7 @@


  col_types                     = NULL,
  guess_type                    = TRUE,
  guess_max                     = 1000L,
  guess_max                     = 1000,
  http_response_encoding        = "UTF-8",
  locale                        = readr::default_locale(),
  verbose                       = TRUE,

@@ -223,7 +224,7 @@

  checkmate::assert_logical( blank_for_gray_form_status , any.missing=FALSE, len=1)

  checkmate::assert_logical(  guess_type                , any.missing=FALSE, len=1)
  checkmate::assert_integerish(guess_max                , any.missing=FALSE, len=1, lower=1)
  checkmate::assert_numeric(   guess_max                , any.missing=FALSE, len=1, lower=1)
  checkmate::assert_character(http_response_encoding    , any.missing=FALSE,     len=1)

  checkmate::assert_class(    locale, "locale"          , null.ok = FALSE)

@@ -4,7 +4,27 @@

#' pattern of a 32-character hexadecimal value.
#' Each character must be an (a) digit 0-9, (b) uppercase letter A-F, or
#' (c) lowercase letter a-f.
#' #' Trailing line endings are removed.
#' Trailing line endings are removed.
#'
#' A typical user does not call this function directly.  However functions like
#' [`redcap_read()`](redcap_read) call it to provide a more informative
#' error message to the user.
#'
#' Some institutions create their own tokens not the standard
#' 32-character hexadecimal value.  The pattern that validates their tokens
#' can be specified with the system environmental variable
#' `REDCAP_TOKEN_PATTERN` using
#' [`base::Sys.setenv()`](base::Sys.setenv).
#'
#' For example, the following regex pattern captures a
#' [base64 encoded value]() with 40 characters:
#' `^([A-Za-z\\d+/\\+=]{40})$`.
#' See <https://regexland.com/base64/> for alternative approaches to validate
#' base64 values.
#'
#' If no pattern is specified, the default is 32-character hex token:
#' `^([0-9A-Fa-f]{32})(?:\\n)?$`.  The important segment is contained in the
#' first (and only) capturing group.  Any trailing newline character is removed.
#'
#' @param token The REDCap token. Required.
#'

@@ -22,23 +42,41 @@

#' REDCapR::sanitize_token(secret_token_1)
#' REDCapR::sanitize_token(secret_token_2)
#' REDCapR::sanitize_token(secret_token_3)
#'
#' # Some institutions use a token system that follows a different pattern
#' Sys.setenv("REDCAP_TOKEN_PATTERN" = "^([A-Za-z\\d+/\\+=]{10})$")
#'
#' secret_token_4 <- "abcde1234="
#' REDCapR::sanitize_token(secret_token_4)
#' Sys.getenv("REDCAP_TOKEN_PATTERN")
#' Sys.unsetenv("REDCAP_TOKEN_PATTERN")

#' @export
sanitize_token <- function(token) {
  pattern <- "^([0-9A-Fa-f]{32})(?:\\n)?$"
  checkmate::assert_character(token, any.missing = TRUE, len = 1)

  pattern_env <- Sys.getenv("REDCAP_TOKEN_PATTERN")
  pattern <-
    if (pattern_env != "") {
      checkmate::assert_character(pattern_env, any.missing = FALSE, len = 1)
      pattern_env
    } else {
      "^([0-9A-Fa-f]{32})(?:\\n)?$"
    }

  if (is.na(token)) {
    stop(
      "The token is `NA`, not a valid 32-character hexademical value."
      "The token is `NA`, which is not allowed."
    )
  } else if (nchar(token) == 0L) {
    stop(
      "The token is an empty string, ",
      "not a valid 32-character hexademical value."
      "The token is an empty string, which is not allowed."
    )
  } else if (!grepl(pattern, token, perl = TRUE)) {
    stop(
      "The token is not a valid 32-character hexademical value."
      "The token does not conform with the regex `",
      pattern,
      "`."
    )
  }


Files		•	•	•	Coverage
R	2,047	1,961	0	86	95.80%
Project Totals (38 files)	2,047	1,961	0	86	95.80%

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comment: false

coverage:
  status:
    project:
      default:
        target: auto
        threshold: 3%
    patch:
      default:
        target: auto
        threshold: 3%

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71	71		filter_logic = "",
72	72
73	73		guess_type = TRUE,
74		-	guess_max = 1000L,
	74	+	guess_max = 1000,
75	75		verbose = TRUE,
76	76		config_options = NULL
77	77		) {

127	128
128	129		col_types = NULL,
129	130		guess_type = TRUE,
130		-	guess_max = 1000L,
	131	+	guess_max = 1000,
131	132		verbose = TRUE,
132	133		config_options = NULL
133	134		) {

142	143		checkmate::assert_logical( export_checkbox_label , any.missing=FALSE, len=1)
143	144
144	145		checkmate::assert_logical( guess_type , any.missing=FALSE, len=1)
145		-	checkmate::assert_integerish(guess_max , any.missing=FALSE, len=1, lower=1)
	146	+	checkmate::assert_numeric( guess_max , any.missing=FALSE, len=1, lower=1)
146	147		checkmate::assert_logical( verbose , any.missing=FALSE, len=1, null.ok=TRUE)
147	148		checkmate::assert_list( config_options , any.missing=TRUE , null.ok=TRUE)
148	149

193	193		checkmate::assert_logical( blank_for_gray_form_status , any.missing=FALSE, len=1)
194	194
195	195		# placeholder: checkmate::assert_logical( guess_type , any.missing=FALSE, len=1)
196		-	# placeholder: checkmate::assert_integerish(guess_max , any.missing=FALSE, len=1, lower=1)
	196	+	# placeholder: checkmate::assert_numeric( guess_max , any.missing=FALSE, len=1, lower=1)
197	197		checkmate::assert_logical( verbose , any.missing=FALSE, len=1, null.ok=TRUE)
198	198		checkmate::assert_list( config_options , any.missing=TRUE , null.ok=TRUE)
199	199

192	193
193	194		col_types = NULL,
194	195		guess_type = TRUE,
195		-	guess_max = 1000L,
	196	+	guess_max = 1000,
196	197		http_response_encoding = "UTF-8",
197	198		locale = readr::default_locale(),
198	199		verbose = TRUE,

34	34		#' unsuccessful operation, it should contain diagnostic information.
35	35		#' * `elapsed_seconds`: The duration of the function.
36	36		#'
37		-	#'
38	37		#' @author Jonathan M. Mang
39	38		#' @references The official documentation can be found on the 'API Help Page'
40	39		#' and 'API Examples' pages on the REDCap wiki (i.e.,

110	109		kernel$status_code
111	110		)
112	111
113		-	# ds <- dplyr::mutate_if(
114		-	# ds,
115		-	# is.character,
116		-	# function(x) dplyr::coalesce(x, "") #Replace NAs with blanks
117		-	# )
118		-	#
119		-	# ds <- dplyr::mutate_if(
120		-	# ds,
121		-	# is.character,
122		-	# function( x ) gsub("\r\n", "\n", x, perl=TRUE)
123		-	# )
124		-	# ds <- dplyr::mutate_if(
125		-	# ds,
126		-	# function( x) inherits(x, "Date"),
127		-	# as.character
128		-	# )
129		-	#
130		-	# ds <- base::as.data.frame(ds)
131		-
132	112		# If an operation is successful, the `raw_text` is no longer returned to
133	113		# save RAM. The content is not really necessary with httr's status
134	114		# message exposed.

28	28		#' @param guess_type A boolean value indicating if all columns should be
29	29		#' returned as character. If false, [readr::read_csv()] guesses the intended
30	30		#' data type for each column. Ignored if `col_types` is not null.
31		-	#' @param guess_max A positive integer passed to [readr::read_csv()] that
	31	+	#' @param guess_max A positive [base::numeric] value
	32	+	#' passed to [readr::read_csv()] that
32	33		#' specifies the maximum number of records to use for guessing column types.
33	34		#' @param verbose A boolean value indicating if `message`s should be printed
34	35		#' to the R console during the operation. The verbose output might contain

4	4		#' pattern of a 32-character hexadecimal value.
5	5		#' Each character must be an (a) digit 0-9, (b) uppercase letter A-F, or
6	6		#' (c) lowercase letter a-f.
7		-	#' #' Trailing line endings are removed.
	7	+	#' Trailing line endings are removed.
	8	+	#'
	9	+	#' A typical user does not call this function directly. However functions like
	10	+	#' [`redcap_read()`](redcap_read) call it to provide a more informative
	11	+	#' error message to the user.
	12	+	#'
	13	+	#' Some institutions create their own tokens not the standard
	14	+	#' 32-character hexadecimal value. The pattern that validates their tokens
	15	+	#' can be specified with the system environmental variable
	16	+	#' `REDCAP_TOKEN_PATTERN` using
	17	+	#' [`base::Sys.setenv()`](base::Sys.setenv).
	18	+	#'
	19	+	#' For example, the following regex pattern captures a
	20	+	#' [base64 encoded value]() with 40 characters:
	21	+	#' `^([A-Za-z\\d+/\\+=]{40})$`.
	22	+	#' See <https://regexland.com/base64/> for alternative approaches to validate
	23	+	#' base64 values.
	24	+	#'
	25	+	#' If no pattern is specified, the default is 32-character hex token:
	26	+	#' `^([0-9A-Fa-f]{32})(?:\\n)?$`. The important segment is contained in the
	27	+	#' first (and only) capturing group. Any trailing newline character is removed.
8	28		#'
9	29		#' @param token The REDCap token. Required.
10	30		#'

22	42		#' REDCapR::sanitize_token(secret_token_1)
23	43		#' REDCapR::sanitize_token(secret_token_2)
24	44		#' REDCapR::sanitize_token(secret_token_3)
	45	+	#'
	46	+	#' # Some institutions use a token system that follows a different pattern
	47	+	#' Sys.setenv("REDCAP_TOKEN_PATTERN" = "^([A-Za-z\\d+/\\+=]{10})$")
	48	+	#'
	49	+	#' secret_token_4 <- "abcde1234="
	50	+	#' REDCapR::sanitize_token(secret_token_4)
	51	+	#' Sys.getenv("REDCAP_TOKEN_PATTERN")
	52	+	#' Sys.unsetenv("REDCAP_TOKEN_PATTERN")
25	53
26	54		#' @export
27	55		sanitize_token <- function(token) {
28		-	pattern <- "^([0-9A-Fa-f]{32})(?:\\n)?$"
	56	+	checkmate::assert_character(token, any.missing = TRUE, len = 1)
	57	+
	58	+	pattern_env <- Sys.getenv("REDCAP_TOKEN_PATTERN")
	59	+	pattern <-
	60	+	if (pattern_env != "") {
	61	+	checkmate::assert_character(pattern_env, any.missing = FALSE, len = 1)
	62	+	pattern_env
	63	+	} else {
	64	+	"^([0-9A-Fa-f]{32})(?:\\n)?$"
	65	+	}
29	66
30	67		if (is.na(token)) {
31	68		stop(
32		-	"The token is `NA`, not a valid 32-character hexademical value."
	69	+	"The token is `NA`, which is not allowed."
33	70		)
34	71		} else if (nchar(token) == 0L) {
35	72		stop(
36		-	"The token is an empty string, ",
37		-	"not a valid 32-character hexademical value."
	73	+	"The token is an empty string, which is not allowed."
38	74		)
39	75		} else if (!grepl(pattern, token, perl = TRUE)) {
40	76		stop(
41		-	"The token is not a valid 32-character hexademical value."
	77	+	"The token does not conform with the regex `",
	78	+	pattern,
	79	+	"`."
42	80		)
43	81		}
44	82

1	comment: false
2
3	coverage:
4	status:
5	project:
6	default:
7	target: auto
8	threshold: 3%
9	patch:
10	default:
11	target: auto
12	threshold: 3%

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