Merge pull request #7 from atorus-research/dev

Get actions to pass

.Rprofile

@@ -1 +1 @@
-source("renv/activate.R")
+# source("renv/activate.R")

DESCRIPTION

@@ -13,7 +13,7 @@ Authors@R: c(
  email = "nmasel@its.jnj.com",
  role = "aut")
  )
-Description: R package for reading and writing CDISC Dataset JSON files
+Description: R package for reading and writing CDISC Dataset JSON files.
 License: Apache License (>= 2)
 URL: https://github.com/atorus-research/datasetjson
 BugReports: https://github.com/atorus-research/datasetjson/issues
@@ -25,6 +25,7 @@ RoxygenNote: 7.2.3
 Depends: R (>= 3.5)
 Imports:
  jsonlite (>= 1.8.7),
+ jsonvalidate (>= 1.3.2)
 Suggests:
  testthat (>= 2.1.0),
  knitr,

NAMESPACE

@@ -25,3 +25,4 @@ importFrom(jsonlite,fromJSON)
 importFrom(jsonlite,toJSON)
 importFrom(jsonvalidate,json_validate)
 importFrom(tools,file_path_sans_ext)
+importFrom(utils,tail)

R/data.R

@@ -20,28 +20,40 @@
 #' Valid SAS(c) date formats pulled from
 #' https://documentation.sas.com/doc/en/vdmmlcdc/8.1/ds2pg/p0bz5detpfj01qn1kz2in7xymkdl.htm
 #'
-#' @format ## `sas_date_formats` A character vector with 45 elements
+#' @format ## `sas_date_formats`
+#' \describe{
+#' A character vector with 45 elements
+#' }
 "sas_date_formats"
 
 #' A List of valid SAS(c) datetime formats
 #'
 #' Valid SAS(c) datetime formats pulled from
 #' https://documentation.sas.com/doc/en/vdmmlcdc/8.1/ds2pg/p0bz5detpfj01qn1kz2in7xymkdl.htm
 #'
-#' @format ## `sas_datetime_formats` A character vector with 7 elements
+#' @format ## `sas_datetime_formats`
+#' \describe{
+#' A character vector with 7 elements
+#' }
 "sas_datetime_formats"
 
 #' A List of valid SAS(c) time formats
 #'
 #' Valid SAS(c) time formats pulled from
 #' https://documentation.sas.com/doc/en/vdmmlcdc/8.1/ds2pg/p0bz5detpfj01qn1kz2in7xymkdl.htm
 #'
-#' @format ## `sas_time_formats` A character vector with 4 elements
+#' @format ## `sas_time_formats`
+#' \describe{
+#' A character vector with 4 elements
+#' }
 "sas_time_formats"
 
 #' Dataset JSON Schema Version 1.0.0
 #'
 #' This object is a character vector holding the schema for Dataset JSON Version 1.0.0
 #'
-#' @format ## `schema_1_0_0` A character vector with 1 element
+#' @format ## `schema_1_0_0`
+#' \describe{
+#' A character vector with 1 element
+#' }
 "schema_1_0_0"

R/data_metadata.R

@@ -1,8 +1,6 @@
 #' Create the data metadata container for a Dataset JSON object
 #'
-#' @param data_type Type of data being written. clinicalData for subject level
-#' data, and referenceData for non-subject level data (i.e. TDMs, Associated
-#' Persons)
+#' @param study Study OID value
 #' @param metadata_version Metadata version OID value
 #' @param metadata_ref Metadata reference (i.e. path to Define.xml)
 #'
@@ -43,8 +41,7 @@ data_metadata <- function(study = "NA", metadata_version = "NA", metadata_ref =
 #' This set of functions
 #' @param x data metadata or datasetjson object
 #' @param study Study OID value
-#'
-#' @param ...
+#' @param ... Additional parameters
 #'
 #' @return A datasetjson or data_metadata object
 #' @export
@@ -64,15 +61,15 @@ set_study_oid <- function(x, study, ...) {
 #' @family Data metadata setters
 #' @rdname data_metadata_setters
 #' @export
-set_study_oid.data_metadata <- function(x, study) {
+set_study_oid.data_metadata <- function(x, study, ...) {
  stopifnot_data_metadata(x)
  x[['studyOID']] <- study
  x
 }
 
 #' @export
 #' @noRd
-set_study_oid.datasetjson <- function(x, study) {
+set_study_oid.datasetjson <- function(x, study, ...) {
  stopifnot_datasetjson(x)
  data_type <- get_data_type(x)
  x[[data_type]][['studyOID']] <- study
@@ -89,15 +86,15 @@ set_metadata_version <- function(x, metadata_version, ...) {
 
 #' @export
 #' @noRd
-set_metadata_version.data_metadata <- function(x, metadata_version) {
+set_metadata_version.data_metadata <- function(x, metadata_version, ...) {
  stopifnot_data_metadata(x)
  x[['metaDataVersionOID']] <- metadata_version
  x
 }
 
 #' @export
 #' @noRd
-set_metadata_version.datasetjson <- function(x, metadata_version) {
+set_metadata_version.datasetjson <- function(x, metadata_version, ...) {
  stopifnot_datasetjson(x)
  data_type <- get_data_type(x)
  x[[data_type]][['metaDataVersionOID']] <- metadata_version

R/dataset_metadata.R

@@ -85,7 +85,7 @@ set_item_data <- function(x, .data, ...) {
 #' @noRd
 #' @export
 #' @method set_item_data dataset_metadata
-set_item_data.dataset_metadata <- function(x, .data) {
+set_item_data.dataset_metadata <- function(x, .data, ...) {
  stopifnot_dataset_metadata(x)
 
  if (!inherits(.data, "data.frame")) {
@@ -187,39 +187,3 @@ df_to_list_rows <- function(x) {
  y[!is.na(y)]
  })
 }
-
-#' Apply JSON metadata to dataframe as attributes
-#'
-#' This function takes supplied metadata and applies it to a dataframe as
-#' corresponding attributes
-#'
-#' @param .data A Dataframe
-#' @param metadata A list containing Dataset JSON dataset object metadata
-#'
-#' @return dataframe
-#' @examples
-#' # TODO:
-#' @noRd
-apply_dataset_metadata <- function(.data, metadata) {
- # TODO: Set records, name, and label to the dataframe as a whole
-
- # TODO: Set OID, name, label, type, length, and format, and keySequence as
- # necessary to each variable
- TRUE
-}
-
-#' Gather Dataset JSON metadata from a dataframe which has Dataset JSON metadata
-#' applied
-#'
-#' This function will gather the attributes from a data frame which has Dataset
-#' JSON metadata applied.
-#'
-#' @param .data A dataframe with Dataset JSON attributes applied
-#'
-#' @return A list of Dataset dataset object JSON metadata
-#' @noRd
-gather_dataset_metadata <- function(.data) {
-
- # Retrieve the necessary metadata off of a data frame that pertains to a dataset JSON object
- TRUE
-}

R/file_metadata.R

@@ -15,7 +15,6 @@
 #' @examples
 #' # Create using parameters
 #' file_meta <- file_metadata(
-#' "clinicalData",
 #' originator = "Some Org",
 #' sys = "source system",
 #' sys_version = "1.0"
@@ -24,8 +23,7 @@
 #' # Set parameters after
 #' file_meta <- file_metadata()
 #'
-#' file_meta_updated <- set_data_type(file_meta, "referenceData")
-#' file_meta_updated <- set_file_oid(file_meta_updated, "/some/path")
+#' file_meta_updated <- set_file_oid(file_meta, "/some/path")
 #' file_meta_updated <- set_originator(file_meta_updated, "Some Org")
 #' file_meta_updated <- set_source_system(file_meta_updated, "source system", "1.0")
 file_metadata <- function(originator="NA", sys = "NA", sys_version = "NA", version = "1.0.0") {
@@ -76,7 +74,9 @@ get_datetime <- function() {
 #' generated the Dataset-JSON file."
 #' @param file_oid fileOID parameter, defined as "A unique identifier for this
 #' file."
-#' @param data_type
+#' @param data_type Type of data being written. clinicalData for subject level
+#' data, and referenceData for non-subject level data (i.e. TDMs, Associated
+#' Persons)
 #'
 #' @return datasetjson or file_metadata object
 #' @export
@@ -86,8 +86,7 @@ get_datetime <- function() {
 #' @examples
 #' file_meta <- file_metadata()
 #'
-#' file_meta_updated <- set_data_type(file_meta, "referenceData")
-#' file_meta_updated <- set_file_oid(file_meta_updated, "/some/path")
+#' file_meta_updated <- set_file_oid(file_meta, "/some/path")
 #' file_meta_updated <- set_originator(file_meta_updated, "Some Org")
 #' file_meta_updated <- set_source_system(file_meta_updated, "source system", "1.0")
 set_source_system <- function(x, sys, sys_version) {

R/global.R

@@ -1 +1,5 @@
-globalVariables()
+globalVariables(c(
+ "schema_1_0_0",
+ "sas_date_formats",
+ "sas_datetime_formats"
+))

R/utils.R

@@ -24,7 +24,7 @@ stopifnot_data_metadata <- function(x) {
 
 stopifnot_file_metadata <- function(x) {
  if (!(inherits(x, "datasetjson") | inherits(x, "file_metadata"))) {
- stop("x must be a datasetjson object or file_metadata object", call.=FALSE)
+ stop("Input must be a datasetjson object or file_metadata object", call.=FALSE)
  }
 }
 

R/zzz.R

@@ -1,6 +1,7 @@
 #' @importFrom jsonvalidate json_validate
 #' @importFrom jsonlite fromJSON toJSON
 #' @importFrom tools file_path_sans_ext
+#' @importFrom utils tail
 NULL
 
 #' @keywords internal

renv.lock

@@ -1,6 +1,6 @@
 {
  "R": {
- "Version": "4.3.0",
+ "Version": "4.2.1",
  "Repositories": [
  {
  "Name": "CRAN",