From a32f53dd70380dd79c3faa20cf8d8af251829fd8 Mon Sep 17 00:00:00 2001
From: mstackhouse <Mike.Stackhouse@atorusresearch.com>
Date: Thu, 5 Sep 2024 11:47:46 -0400
Subject: [PATCH 1/8] New schema

---
 data/schema_1_0_0.rda | Bin 1444 -> 0 bytes
 data/schema_1_1_0.rda | Bin 0 -> 1951 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 data/schema_1_0_0.rda
 create mode 100644 data/schema_1_1_0.rda

diff --git a/data/schema_1_0_0.rda b/data/schema_1_0_0.rda
deleted file mode 100644
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From 64c29876f4f467cf3d5fd9e9f990828efa09f159 Mon Sep 17 00:00:00 2001
From: mstackhouse <Mike.Stackhouse@atorusresearch.com>
Date: Thu, 5 Sep 2024 12:58:03 -0400
Subject: [PATCH 2/8] save progress in reformatting dataset metadata

---
 R/archive/data_metadata.R |  56 +++++++++
 R/data.R                  |   4 +-
 R/data_metadata.R         | 138 ---------------------
 R/datasetjson.R           |  16 +--
 R/file_metadata.R         | 247 ++++++++++++++++++++++++--------------
 R/validate_dataset_json.R |   4 +-
 data-raw/data.R           |   6 +-
 7 files changed, 226 insertions(+), 245 deletions(-)
 create mode 100644 R/archive/data_metadata.R
 delete mode 100644 R/data_metadata.R

diff --git a/R/archive/data_metadata.R b/R/archive/data_metadata.R
new file mode 100644
index 0000000..1ab098a
--- /dev/null
+++ b/R/archive/data_metadata.R
@@ -0,0 +1,56 @@
+#' Create the data metadata container for a Dataset JSON object
+#'
+#' @param study Study OID value
+#' @param metadata_version Metadata version OID value
+#' @param metadata_ref Metadata reference (i.e. path to Define.xml)
+#'
+#' @return data_metadata object
+#' @export
+#'
+#' @examples
+#' # Create object directly
+#' data_meta <- data_metadata(
+#'   study = "SOMESTUDY",
+#'   metadata_version = "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7",
+#'   metadata_ref = "some/define.xml"
+#' )
+#'
+#' # Use setter functions
+#' data_meta <- data_metadata()
+#' data_meta_updated <- set_metadata_ref(data_meta, "some/define.xml")
+#' data_meta_updated <- set_metadata_version(data_meta_updated, "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7")
+#' data_meta_updated <- set_study_oid(data_meta_updated, "SOMESTUDY")
+#'
+data_metadata <- function(study = NULL, metadata_version = NULL, metadata_ref = NULL) {
+
+  x <- list(
+    studyOID = study,
+    metaDataVersionOID = metadata_version,
+    metaDataRef = metadata_ref,
+    itemGroupData = NULL
+  )
+
+  structure(
+    x,
+    class = c("data_metadata", "list")
+  )
+}
+
+#' Set data metadata parameters
+#'
+#' This set of functions
+#' @param x data metadata or datasetjson object
+#' @param study Study OID value
+#' @param ... Additional parameters
+#'
+#' @return A datasetjson or data_metadata object
+#' @export
+#'
+#' @family Data metadata setters
+#' @rdname data_metadata_setters
+#'
+#' @examples
+#' data_meta <- data_metadata()
+#' data_meta_updated <- set_metadata_ref(data_meta, "some/define.xml")
+#' data_meta_updated <- set_metadata_version(data_meta_updated, "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7")
+#' data_meta_updated <- set_study_oid(data_meta_updated, "SOMESTUDY")
\ No newline at end of file
diff --git a/R/data.R b/R/data.R
index bc658f8..7f2b9be 100644
--- a/R/data.R
+++ b/R/data.R
@@ -48,9 +48,9 @@
 #' }
 "sas_time_formats"
 
-#' Dataset JSON Schema Version 1.0.0
+#' Dataset JSON Schema Version 1.1.0
 #'
-#' This object is a character vector holding the schema for Dataset JSON Version 1.0.0
+#' This object is a character vector holding the schema for Dataset JSON Version 1.1.0
 #'
 #' @format ## `schema_1_0_0`
 #' \describe{
diff --git a/R/data_metadata.R b/R/data_metadata.R
deleted file mode 100644
index 0bf84d2..0000000
--- a/R/data_metadata.R
+++ /dev/null
@@ -1,138 +0,0 @@
-#' Create the data metadata container for a Dataset JSON object
-#'
-#' @param study Study OID value
-#' @param metadata_version Metadata version OID value
-#' @param metadata_ref Metadata reference (i.e. path to Define.xml)
-#'
-#' @return data_metadata object
-#' @export
-#'
-#' @examples
-#' # Create object directly
-#' data_meta <- data_metadata(
-#'   study = "SOMESTUDY",
-#'   metadata_version = "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7",
-#'   metadata_ref = "some/define.xml"
-#' )
-#'
-#' # Use setter functions
-#' data_meta <- data_metadata()
-#' data_meta_updated <- set_metadata_ref(data_meta, "some/define.xml")
-#' data_meta_updated <- set_metadata_version(data_meta_updated, "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7")
-#' data_meta_updated <- set_study_oid(data_meta_updated, "SOMESTUDY")
-#'
-data_metadata <- function(study = NULL, metadata_version = NULL, metadata_ref = NULL) {
-
-  x <- list(
-    studyOID = study,
-    metaDataVersionOID = metadata_version,
-    metaDataRef = metadata_ref,
-    itemGroupData = NULL
-  )
-
-  structure(
-    x,
-    class = c("data_metadata", "list")
-  )
-}
-
-#' Set data metadata parameters
-#'
-#' This set of functions
-#' @param x data metadata or datasetjson object
-#' @param study Study OID value
-#' @param ... Additional parameters
-#'
-#' @return A datasetjson or data_metadata object
-#' @export
-#'
-#' @family Data metadata setters
-#' @rdname data_metadata_setters
-#'
-#' @examples
-#' data_meta <- data_metadata()
-#' data_meta_updated <- set_metadata_ref(data_meta, "some/define.xml")
-#' data_meta_updated <- set_metadata_version(data_meta_updated, "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7")
-#' data_meta_updated <- set_study_oid(data_meta_updated, "SOMESTUDY")
-set_study_oid <- function(x, study, ...) {
-  UseMethod("set_study_oid")
-}
-
-#' @export
-#' @noRd
-set_study_oid.data_metadata <- function(x, study, ...) {
-  x[['studyOID']] <- study
-  x
-}
-
-#' @export
-#' @noRd
-set_study_oid.datasetjson <- function(x, study, ...) {
-  data_type <- get_data_type(x)
-  x[[data_type]][['studyOID']] <- study
-  x
-}
-
-#' @export
-#' @noRd
-set_study_oid.default <- function(x, study, ...) {
-  stopifnot_data_metadata(x)
-}
-
-#' @param metadata_version Metadata version OID value
-#' @family Data metadata setters
-#' @rdname data_metadata_setters
-#' @export
-set_metadata_version <- function(x, metadata_version, ...) {
-  UseMethod("set_metadata_version")
-}
-
-#' @export
-#' @noRd
-set_metadata_version.data_metadata <- function(x, metadata_version, ...) {
-  x[['metaDataVersionOID']] <- metadata_version
-  x
-}
-
-#' @export
-#' @noRd
-set_metadata_version.datasetjson <- function(x, metadata_version, ...) {
-  data_type <- get_data_type(x)
-  x[[data_type]][['metaDataVersionOID']] <- metadata_version
-  x
-}
-
-#' @export
-#' @noRd
-set_metadata_version.default <- function(x, metadata_version, ...) {
-  stopifnot_data_metadata(x)
-}
-
-#' @param metadata_ref Metadata reference (i.e. path to Define.xml)
-#' @family Data metadata setters
-#' @rdname data_metadata_setters
-#' @export
-set_metadata_ref <- function(x, metadata_ref) {
-  UseMethod("set_metadata_ref")
-}
-
-#' @export
-#' @noRd
-set_metadata_ref.data_metadata <- function(x, metadata_ref) {
-  x[['metaDataRef']] <- metadata_ref
-  x
-}
-
-#' @export
-#' @noRd
-set_metadata_ref.datasetjson <- function(x, metadata_ref) {
-  data_type <- get_data_type(x)
-  x[[data_type]][['metaDataRef']] <- metadata_ref
-  x
-}
-
-#' @export
-#' @noRd
-set_metadata_ref.default <- function(x, metadata_ref) {
-  stopifnot_data_metadata(x)
-}
diff --git a/R/datasetjson.R b/R/datasetjson.R
index 9b015ac..4a32dd5 100644
--- a/R/datasetjson.R
+++ b/R/datasetjson.R
@@ -65,7 +65,7 @@
 #'   data_meta = data_meta
 #'   )
 dataset_json <- function(.data, item_id, name, label, items, dataset_meta,
-                         version="1.0.0", data_type = c('clinicalData', 'referenceData'),
+                         version="1.1.0", data_type = c('clinicalData', 'referenceData'),
                          file_meta = file_metadata(),
                          data_meta = data_metadata()
                          ) {
@@ -85,24 +85,24 @@ dataset_json <- function(.data, item_id, name, label, items, dataset_meta,
 new_dataset_json <- function(version, item_id, data_type, name, label, items,
                              dataset_meta, file_meta, data_meta, .data) {
 
-  if (!(version %in% c("1.0.0"))) {
-    stop("Unsupported version specified - currently only version 1.0.0 is supported", call.=FALSE)
+  if (!(version %in% c("1.1.0"))) {
+    stop("Unsupported version specified - currently only version 1.1.0 is supported", call.=FALSE)
   }
 
   # List of version specific generators
   funcs <- list(
-    "1.0.0" = new_dataset_json_v1_0_0
+    "1.1.0" = new_dataset_json_v1_1_0
   )
 
   # Extract the function and call it to return the base structure
   funcs[[version]](item_id, data_type, name, label, items, dataset_meta, file_meta, data_meta, .data)
 }
 
-#' Dataset JSON v1.0.0 Generator
+#' Dataset JSON v1.1.0 Generator
 #'
-#' @return datasetjson_v1_0_0 object
+#' @return datasetjson_v1_1_0 object
 #' @noRd
-new_dataset_json_v1_0_0 <- function(item_id, data_type, name, label, items, dataset_meta, file_meta, data_meta, .data) {
+new_dataset_json_v1_1_0 <- function(item_id, data_type, name, label, items, dataset_meta, file_meta, data_meta, .data) {
 
   if (missing(dataset_meta)) {
     if (any(missing(item_id), missing(name), missing(label), missing(items))) {
@@ -123,6 +123,6 @@ new_dataset_json_v1_0_0 <- function(item_id, data_type, name, label, items, data
 
   structure(
     ds_json,
-    class = c("datasetjson_v1_0_0", "datasetjson", "list")
+    class = c("datasetjson_v1_1_0", "datasetjson", "list")
   )
 }
diff --git a/R/file_metadata.R b/R/file_metadata.R
index 10a2f1f..51f0c97 100644
--- a/R/file_metadata.R
+++ b/R/file_metadata.R
@@ -1,69 +1,6 @@
-#' Create a file metadata object
+#' Dataset Metadata Setters
 #'
-#' @param originator originator parameter, defined as "The organization that
-#'   generated the Dataset-JSON file."
-#' @param sys sourceSystem parameter, defined as "The computer system or
-#'   database management system that is the source of the information in this
-#'   file."
-#' @param sys_version sourceSystemVersion, defined as "The version of the
-#'   sourceSystem"
-#' @param file_oid fileOID parameter, defined as "A unique identifier for this
-#'   file."
-#' @param version Dataset JSON schema version being used
-#'
-#' @return file_metadata object
-#' @export
-#'
-#' @examples
-#' # Create using parameters
-#' file_meta <- file_metadata(
-#'     originator = "Some Org",
-#'     sys = "source system",
-#'     sys_version = "1.0"
-#'   )
-#'
-#' # Set parameters after
-#' file_meta <- file_metadata()
-#'
-#' 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=NULL, sys = NULL, sys_version = NULL, file_oid = NULL, version = "1.0.0") {
-
-  if (!(version %in% c("1.0.0"))) {
-    stop("Unsupported version specified - currently only version 1.0.0 is supported", call.=FALSE)
-  }
-
-  x <- list(
-    "creationDateTime"= character(),
-    "datasetJSONVersion"= version,
-    "fileOID" = file_oid,
-    "asOfDateTime" = NULL, # Not sure we want this to exist?
-    "originator" = originator,
-    "sourceSystem" = sys,
-    "sourceSystemVersion" = sys_version
-  )
-
-  structure(
-    x,
-    class = c("file_metadata", "list")
-  )
-}
-
-#' Create an ISO8601 formatted datetime of the current time
-#'
-#' This is used to create the creationDateTime and asOfDateTime attributes of
-#' the Dataset JSON object, called at the appropriate time for each attribute
-#'
-#' @return ISO8601 formatted datetime
-#' @noRd
-get_datetime <- function() {
-  format(Sys.time(), "%Y-%m-%dT%H:%M:%S")
-}
-
-#' File Metadata Setters
-#'
-#' Set information about the file and source system used to generate the Dataset
+#' Set information about the file, source system, study, and dataset used to generate the Dataset
 #' JSON object.
 #'
 #' @details
@@ -86,54 +23,180 @@ get_datetime <- function() {
 #'   generated the Dataset-JSON file."
 #' @param file_oid fileOID parameter, defined as "A unique identifier for this
 #'   file."
-#' @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)
+#' @param item_oid ID used to label dataset with the itemGroupData parameter.
+#'   Defined as "Object of Datasets. Key value is a unique identifier for
+#'   Dataset, corresponding to ItemGroupDef/@OID in Define-XML."
+#' @param name Dataset name
+#' @param dataset_label Dataset Label
 #'
-#' @return datasetjson or file_metadata object
+#' @return datasetjson object
 #' @export
-#' @family File Metadata Setters
-#' @rdname file_metadata_setters
+#' @family Dataset Metadata Setters
+#' @rdname dataset_metadata_setters
 #'
 #' @examples
-#' file_meta <- file_metadata()
+#' ds_json <- dataset_json(iris)
+#' 
+#' ds_json <- set_dataset_metadata(
+#'   iris, 
+#'   file_oid = "/some/path"
+#'   originator = "Some Org", 
+#'   sys = "source system", 
+#'   sys_version = "1.0", 
+#'   study = "SOMESTUDY",
+#'   metadata_version = "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7",
+#'   metadata_ref = "some/define.xml",
+#'   item_oid = "IG.IRIS",
+#'   name = "IRIS",
+#'   dataset_label = "Iris"
+#' )
 #'
-#' 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")
+#' # Individual Elements
+#' ds_json <- dataset_json(iris)
+#' ds_json <- set_file_oid(ds_json, "/some/path")
+#' ds_json <- set_study_oid(ds_json, "SOMESTUDY")
+#' ds_json <- set_originator(ds_json, "Some Org")
+#' ds_json <- set_source_system(ds_json, "source system", "1.0")
+#' ds_json <- set_metadata_ref(ds_json, "some/define.xml")
+#' ds_json <- set_metadata_version(ds_json, "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7")
+#' ds_json <- set_item_oid(ds_json, "IG.IRIS")
+#' ds_json <- set_dataset_name(ds_json, "IRIS")
+#' ds_json <- set_dataseT_label(ds_json, "Iris")
+set_dataset_metadata <- function(x, file_oid = NULL, originator=NULL, sys = NULL, 
+                                 sys_version = NULL, study=NULL, metadata_version=NULL,
+                                 metadata_ref=NULL, item_oid=NULL, name = NULL, 
+                                 dataset_label=NULL) {
+  stopifnot_datasetjson(x)
+
+  if (!is.null(sys) && !is.null(sys_version)) {
+    attr(x, 'sourceSystem') <- list(
+      "name" = sys,
+      "version" = sys_version
+    )
+  }
+
+  attr(x, 'fileOID') <- file_oid
+  attr(x, 'originator') <- originator
+  attr(x, 'studyOID') <- study
+  attr(x, 'metaDataVersionOID') <- metadata_version
+  attr(x, 'metaDataRef') <- metadata_ref
+  attr(x, "itemGroupOID") <- item_oid
+  attr(x, 'records') <- nrow(x)
+  attr(x, 'name') <- name
+  attr(x, 'label') <- dataset_label
+  attr('isReferenceData') <- FALSE
+  x
+}
+
+#' @export
+#' @family Dataset Metadata Setters
+#' @rdname dataset_metadata_setters
 set_source_system <- function(x, sys, sys_version) {
-  stopifnot_file_metadata(x)
-  x[['sourceSystem']] <- sys
-  x[['sourceSystemVersion']] <- sys_version
+  stopifnot_datasetjson(x)
+  attr(x, 'sourceSystem') <- list(
+    "name" = sys,
+    "version" = sys_version
+  )
   x
 }
 
 #' @export
-#' @family File Metadata Setters
-#' @rdname file_metadata_setters
+#' @family Dataset Metadata Setters
+#' @rdname dataset_metadata_setters
 set_originator <- function(x, originator) {
-  stopifnot_file_metadata(x)
-  x[['originator']] <- originator
+  stopifnot_datasetjson(x)
+  attr(x, 'originator') <- originator
   x
 }
 
 #' @export
-#' @family File Metadata Setters
-#' @rdname file_metadata_setters
+#' @family Dataset Metadata Setters
+#' @rdname dataset_metadata_setters
 set_file_oid <- function(x, file_oid) {
-  stopifnot_file_metadata(x)
-  x[['fileOID']] <- file_oid
+  stopifnot_datasetjson(x)
+  attr(x, 'fileOID') <- file_oid
   x
 }
 
 #' @export
-#' @family File Metadata Setters
-#' @rdname file_metadata_setters
-set_data_type <- function(x, data_type = c('clinicalData', 'referenceData')) {
+#' @family Dataset Metadata Setters
+#' @rdname dataset_metadata_setters
+set_study_oid <- function(x, study) {
   stopifnot_datasetjson(x)
-  data_type = match.arg(data_type)
+  attr(x, 'studyOID') <- study
+  x
+}
+
+#' @export
+#' @family Dataset Metadata Setters
+#' @rdname dataset_metadata_setters
+set_metadata_version <- function(x, metadata_version) {
+  stopifnot_datasetjson(x)
+  attr(x, 'metaDataVersionOID') <- metadata_version
+  x
+}
 
-  # For the clinicalData or referenceData, set the parameter correctly
-  names(x) <- c(names(x[1:7]), data_type)
+#' @export
+#' @family Dataset Metadata Setters
+#' @rdname dataset_metadata_setters
+set_metadata_ref <- function(x, metadata_ref) {
+  stopifnot_datasetjson(x)
+  attr(x, 'metaDataRef') <- metadata_ref
   x
 }
+
+#' @export
+#' @family Dataset Metadata Setters
+#' @rdname dataset_metadata_setters
+set_item_oid <- function(x, item_oid) {
+  stopifnot_datasetjson(x)
+  attr(x, "itemGroupOID") <- item_oid
+}
+
+#' @export
+#' @family Dataset Metadata Setters
+#' @rdname dataset_metadata_setters
+set_dataset_name <- function(x, name) {
+  stopifnot_datasetjson(x)
+  attr(x, 'name') <- name
+}
+
+#' @export
+#' @family Dataset Metadata Setters
+#' @rdname dataset_metadata_setters
+set_dataset_label <- function(x, dataset_label) {
+  stopifnot_datasetjson(x)
+  attr(x, 'label') <- dataset_label
+}
+
+#' Declare as reference data
+#' 
+#' Sets DatasetJSON file to have the isReferenceData attribute set to TRUE
+#' 
+#' @param x datasetjson object
+#' 
+#' @return datasetjson object
+#' @export
+#' 
+#' @examples
+#' ds_json <- dataset_json(iris)
+#' ds_json <- set_as_reference_data(ds_json)
+set_as_reference_data <- function(x) {
+  stopifnot_datasetjson(x)
+  attr(x, 'isReferenceData') <- TRUE
+}
+
+
+#' Create an ISO8601 formatted datetime of the current time
+#'
+#' This is used to create the creationDateTime and asOfDateTime attributes of
+#' the Dataset JSON object, called at the appropriate time for each attribute
+#'
+#' @return ISO8601 formatted datetime
+#' @noRd
+get_datetime <- function() {
+  format(Sys.time(), "%Y-%m-%dT%H:%M:%S")
+}
diff --git a/R/validate_dataset_json.R b/R/validate_dataset_json.R
index ae37d0c..096365d 100644
--- a/R/validate_dataset_json.R
+++ b/R/validate_dataset_json.R
@@ -29,12 +29,12 @@ validate_dataset_json <- function(x) {
     js <- x
   }
 
-  v <- jsonvalidate::json_validate(js, schema_1_0_0, engine="ajv", verbose=TRUE)
+  v <- jsonvalidate::json_validate(js, schema_1_1_0, engine="ajv", verbose=TRUE)
   if (!v) {
     warning("File contains errors!")
     return(attr(v, 'errors'))
   } else {
-    message("File is valid per the Dataset JSON v1.0.0 schema\n")
+    message("File is valid per the Dataset JSON v1.1.0 schema\n")
     data.frame(
       instancePath = character(),
       schemaPath = character(),
diff --git a/data-raw/data.R b/data-raw/data.R
index 83a1dc9..1444d4c 100644
--- a/data-raw/data.R
+++ b/data-raw/data.R
@@ -138,6 +138,6 @@ sas_time_formats <- c(
 usethis::use_data(sas_time_formats, overwrite = TRUE)
 
 # Dataset JSON Schema V1.0.0 as Character Vector
-schema_file <- test_path("testdata", "dataset.schema.json")
-schema_1_0_0 = readChar(schema_file, file.info(schema_file)$size)
-usethis::use_data(schema_1_0_0, overwrite=TRUE)
+schema_file <- testthat::test_path("testdata", "dataset.schema.json")
+schema_1_1_0 = readChar(schema_file, file.info(schema_file)$size)
+usethis::use_data(schema_1_1_0, overwrite=TRUE)

From 945b6621671cb0012c45584a7f6f9097c7789118 Mon Sep 17 00:00:00 2001
From: mstackhouse <Mike.Stackhouse@atorusresearch.com>
Date: Thu, 5 Sep 2024 14:40:29 -0400
Subject: [PATCH 3/8] Modifications for new schema

---
 R/column_classes.R |  32 +++++++++++
 R/data.R           |  37 +-----------
 R/datasetjson.R    | 139 +++++++++++++++++++++++----------------------
 R/file_metadata.R  |  48 +---------------
 R/global.R         |   4 +-
 5 files changed, 106 insertions(+), 154 deletions(-)
 create mode 100644 R/column_classes.R

diff --git a/R/column_classes.R b/R/column_classes.R
new file mode 100644
index 0000000..2e19aac
--- /dev/null
+++ b/R/column_classes.R
@@ -0,0 +1,32 @@
+# This file contains several helpers for reading and writing date / datetime
+# columns from a Dataset JSON file
+
+#' Get the column classes off a data frame
+#'
+#' @param x A data.frame
+#'
+#' @return Named character vector of columns and types
+#' @noRd
+get_column_classes <- function(x) {
+  vapply(x, function(X) class(X)[1], FUN.VALUE=character(1))
+}
+
+#' Get the columns with a class of Date from a data.frame
+#'
+#' @param x A data.frame
+#'
+#' @return A data.frame
+#' @noRd
+get_date_cols <- function(x) {
+  x[get_column_classes(x) == "Date"]
+}
+
+#' Get the columns with a class of POSIXct from a data.frame
+#'
+#' @param x A data.frame
+#'
+#' @return A data.frame
+#' @noRd
+get_datetime_cols <- function(x) {
+  x[get_column_classes(x) == "POSIXct"]
+}
diff --git a/R/data.R b/R/data.R
index 7f2b9be..124a1ef 100644
--- a/R/data.R
+++ b/R/data.R
@@ -15,45 +15,12 @@
 #' }
 "iris_items"
 
-#' A List of valid SAS(c) date formats
-#'
-#' Valid SAS(c) date formats pulled from
-#' https://documentation.sas.com/doc/en/vdmmlcdc/8.1/ds2pg/p0bz5detpfj01qn1kz2in7xymkdl.htm
-#'
-#' @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`
-#' \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`
-#' \describe{
-#'   A character vector with 4 elements
-#' }
-"sas_time_formats"
-
 #' Dataset JSON Schema Version 1.1.0
 #'
 #' This object is a character vector holding the schema for Dataset JSON Version 1.1.0
 #'
-#' @format ## `schema_1_0_0`
+#' @format ## `schema_1_1_0`
 #' \describe{
 #'   A character vector with 1 element
 #' }
-"schema_1_0_0"
+"schema_1_1_0"
diff --git a/R/datasetjson.R b/R/datasetjson.R
index 4a32dd5..840eed0 100644
--- a/R/datasetjson.R
+++ b/R/datasetjson.R
@@ -2,24 +2,30 @@
 #'
 #' Create the base object used to write a Dataset JSON file.
 #'
+#' @details
+#' 
+#' Note that DatasetJSON is on version 1.1.0. Based off findings from the pilot, 
+#' version 1.1.0 reflects feedback from the user community. Support for 1.0.0 has 
+#' been deprecated.
+#' 
 #' @param .data Input data to contain within the Dataset JSON file. Written to
 #'   the itemData parameter.
-#' @param item_id ID used to label dataset with the itemGroupData parameter.
+#' @param sys sourceSystem parameter, defined as "The computer system or
+#'   database management system that is the source of the information in this
+#'   file."
+#' @param sys_version sourceSystemVersion, defined as "The version of the
+#'   sourceSystem"
+#' @param originator originator parameter, defined as "The organization that
+#'   generated the Dataset-JSON file."
+#' @param file_oid fileOID parameter, defined as "A unique identifier for this
+#'   file."
+#' @param study Study OID value
+#' @param metadata_version Metadata version OID value
+#' @param metadata_ref Metadata reference (i.e. path to Define.xml)
+#' @param item_oid ID used to label dataset with the itemGroupData parameter.
 #'   Defined as "Object of Datasets. Key value is a unique identifier for
 #'   Dataset, corresponding to ItemGroupDef/@OID in Define-XML."
-#' @param name Dataset name
-#' @param label Dataset Label
-#' @param items Variable metadata
-#' @param dataset_meta A dataset_metadata object holding pre-specified
-#'   dataset metadata.
-#' @param version Version of Dataset JSON schema to follow.
-#' @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 file_meta A file_metadata object holding pre-specified file
-#'   metadata
-#' @param data_meta A data_metadata object holding pre-specified data
-#'   metadata
+#' @param version The DatasetJSON version to use. Currently only 1.1.0 is supported.
 #'
 #' @return dataset_json object pertaining to the specific Dataset JSON version
 #'   specific
@@ -27,7 +33,19 @@
 #'
 #' @examples
 #' # Create a basic object
-#' ds_json <- dataset_json(iris, "IG.IRIS", "IRIS", "Iris", iris_items)
+#' ds_json <- dataset_json(
+#'   iris, 
+#'   file_oid = "/some/path"
+#'   originator = "Some Org", 
+#'   sys = "source system", 
+#'   sys_version = "1.0", 
+#'   study = "SOMESTUDY",
+#'   metadata_version = "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7",
+#'   metadata_ref = "some/define.xml",
+#'   item_oid = "IG.IRIS",
+#'   name = "IRIS",
+#'   dataset_label = "Iris"
+#' )
 #'
 #' # Attach attributes directly
 #' ds_json_updated <- set_data_type(ds_json, "referenceData")
@@ -37,40 +55,15 @@
 #' ds_json_updated <- set_originator(ds_json_updated, "Some Org")
 #' ds_json_updated <- set_source_system(ds_json_updated, "source system", "1.0")
 #' ds_json_updated <- set_study_oid(ds_json_updated, "SOMESTUDY")
-#'
-#' # Create independent objects for metadata sections first
-#' file_meta <- file_metadata(
-#'   originator = "Some Org",
-#'   sys = "source system",
-#'   sys_version = "1.0"
-#' )
-#'
-#' data_meta <- data_metadata(
-#'   study = "SOMESTUDY",
-#'   metadata_version = "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7",
-#'   metadata_ref = "some/define.xml"
-#' )
-#'
-#' dataset_meta <- dataset_metadata(
-#'   item_id = "IG.IRIS",
-#'   name = "IRIS",
-#'   label = "Iris",
-#'   items = iris_items
-#' )
-#'
-#' ds_json_from_meta <- dataset_json(
-#'   iris,
-#'   dataset_meta = dataset_meta,
-#'   file_meta = file_meta,
-#'   data_meta = data_meta
-#'   )
-dataset_json <- function(.data, item_id, name, label, items, dataset_meta,
-                         version="1.1.0", data_type = c('clinicalData', 'referenceData'),
-                         file_meta = file_metadata(),
-                         data_meta = data_metadata()
-                         ) {
-  data_type = match.arg(data_type)
-  new_dataset_json(version, item_id, data_type, name, label, items, dataset_meta, file_meta, data_meta, .data)
+#' ds_json_updated <- set_item_oid(ds_json_updated, "IG.IRIS")
+#' ds_json_updated <- set_dataset_name(ds_json_updated, "IRIS")
+#' ds_json_updated <- set_dataseT_label(ds_json_updated, "Iris")
+dataset_json <- function(.data, file_oid = NULL, originator=NULL, sys=NULL, 
+                          sys_version = NULL, study=NULL, metadata_version=NULL,
+                          metadata_ref=NULL, item_oid=NULL, name=NULL, 
+                          dataset_label=NULL, version="1.1.0") {
+  new_dataset_json(.data, file_oid, originator, sys, sys_version, study, metadata_version,
+                   metadata_ref, item_oid, name, dataset_label, version)
 }
 
 #' Create a base Dataset JSON Container
@@ -82,8 +75,9 @@ dataset_json <- function(.data, item_id, name, label, items, dataset_meta,
 #' @return datasetjson object
 #'
 #' @noRd
-new_dataset_json <- function(version, item_id, data_type, name, label, items,
-                             dataset_meta, file_meta, data_meta, .data) {
+new_dataset_json <- function(.data, file_oid, originator, sys, sys_version, study, 
+                             metadata_version, metadata_ref, item_oid, name, dataset_label,
+                             version) {
 
   if (!(version %in% c("1.1.0"))) {
     stop("Unsupported version specified - currently only version 1.1.0 is supported", call.=FALSE)
@@ -95,34 +89,41 @@ new_dataset_json <- function(version, item_id, data_type, name, label, items,
   )
 
   # Extract the function and call it to return the base structure
-  funcs[[version]](item_id, data_type, name, label, items, dataset_meta, file_meta, data_meta, .data)
+  funcs[[version]](.data, file_oid, originator, sys, sys_version, study, 
+                   metadata_version, metadata_ref, item_oid, name, dataset_label)
 }
 
 #' Dataset JSON v1.1.0 Generator
 #'
 #' @return datasetjson_v1_1_0 object
 #' @noRd
-new_dataset_json_v1_1_0 <- function(item_id, data_type, name, label, items, dataset_meta, file_meta, data_meta, .data) {
-
-  if (missing(dataset_meta)) {
-    if (any(missing(item_id), missing(name), missing(label), missing(items))) {
-      stop("If dataset_meta is not provided, then name, label, and items must be provided", call.=FALSE)
-    }
+new_dataset_json_v1_1_0 <- function(.data, file_oid, originator, sys, sys_version, study, 
+                                    metadata_version, metadata_ref, item_oid, name, dataset_label) {
 
-    # Create the dataset metadata with provided info
-    dataset_meta <- dataset_metadata(item_id, name, label, items)
+  if (!inherits(.data, 'data.frame')) {
+    stop("datasetjson objects must inherit from a data.frame", call.=FALSE)
   }
 
-  # Attach .data into dataset_meta
-  dataset_meta <- set_item_data(dataset_meta, .data)
-
-  # Combine file_meta, data_meta, and dataset_meta together
-  ds_json <- file_meta
-  ds_json[[data_type]] <- data_meta
-  ds_json[[data_type]][['itemGroupData']] <- dataset_meta
+  if (!is.null(sys) && !is.null(sys_version)) {
+    attr(.data, 'sourceSystem') <- list(
+      "name" = sys,
+      "version" = sys_version
+    )
+  }
 
+  attr(.data, 'fileOID') <- file_oid
+  attr(.data, 'originator') <- originator
+  attr(.data, 'studyOID') <- study
+  attr(.data, 'metaDataVersionOID') <- metadata_version
+  attr(.data, 'metaDataRef') <- metadata_ref
+  attr(.data, "itemGroupOID") <- item_oid
+  attr(.data, 'records') <- nrow(x)
+  attr(.data, 'name') <- name
+  attr(.data, 'label') <- dataset_label
+  attr(.data, 'isReferenceData') <- FALSE
+  
   structure(
-    ds_json,
-    class = c("datasetjson_v1_1_0", "datasetjson", "list")
+    .data,
+    class = c("datasetjson_v1_1_0", "datasetjson", "data.frame")
   )
 }
diff --git a/R/file_metadata.R b/R/file_metadata.R
index 51f0c97..e0ca4cd 100644
--- a/R/file_metadata.R
+++ b/R/file_metadata.R
@@ -39,23 +39,6 @@
 #'
 #' @examples
 #' ds_json <- dataset_json(iris)
-#' 
-#' ds_json <- set_dataset_metadata(
-#'   iris, 
-#'   file_oid = "/some/path"
-#'   originator = "Some Org", 
-#'   sys = "source system", 
-#'   sys_version = "1.0", 
-#'   study = "SOMESTUDY",
-#'   metadata_version = "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7",
-#'   metadata_ref = "some/define.xml",
-#'   item_oid = "IG.IRIS",
-#'   name = "IRIS",
-#'   dataset_label = "Iris"
-#' )
-#'
-#' # Individual Elements
-#' ds_json <- dataset_json(iris)
 #' ds_json <- set_file_oid(ds_json, "/some/path")
 #' ds_json <- set_study_oid(ds_json, "SOMESTUDY")
 #' ds_json <- set_originator(ds_json, "Some Org")
@@ -64,36 +47,7 @@
 #' ds_json <- set_metadata_version(ds_json, "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7")
 #' ds_json <- set_item_oid(ds_json, "IG.IRIS")
 #' ds_json <- set_dataset_name(ds_json, "IRIS")
-#' ds_json <- set_dataseT_label(ds_json, "Iris")
-set_dataset_metadata <- function(x, file_oid = NULL, originator=NULL, sys = NULL, 
-                                 sys_version = NULL, study=NULL, metadata_version=NULL,
-                                 metadata_ref=NULL, item_oid=NULL, name = NULL, 
-                                 dataset_label=NULL) {
-  stopifnot_datasetjson(x)
-
-  if (!is.null(sys) && !is.null(sys_version)) {
-    attr(x, 'sourceSystem') <- list(
-      "name" = sys,
-      "version" = sys_version
-    )
-  }
-
-  attr(x, 'fileOID') <- file_oid
-  attr(x, 'originator') <- originator
-  attr(x, 'studyOID') <- study
-  attr(x, 'metaDataVersionOID') <- metadata_version
-  attr(x, 'metaDataRef') <- metadata_ref
-  attr(x, "itemGroupOID") <- item_oid
-  attr(x, 'records') <- nrow(x)
-  attr(x, 'name') <- name
-  attr(x, 'label') <- dataset_label
-  attr('isReferenceData') <- FALSE
-  x
-}
-
-#' @export
-#' @family Dataset Metadata Setters
-#' @rdname dataset_metadata_setters
+#' ds_json <- set_dataset_label(ds_json, "Iris")
 set_source_system <- function(x, sys, sys_version) {
   stopifnot_datasetjson(x)
   attr(x, 'sourceSystem') <- list(
diff --git a/R/global.R b/R/global.R
index 3bf88eb..089e027 100644
--- a/R/global.R
+++ b/R/global.R
@@ -1,5 +1,3 @@
 globalVariables(c(
-  "schema_1_0_0",
-  "sas_date_formats",
-  "sas_datetime_formats"
+  "schema_1_1_0"
 ))

From 3ace7ac17ce21e0b4329cb6c9d35b0704ce78a85 Mon Sep 17 00:00:00 2001
From: mstackhouse <Mike.Stackhouse@atorusresearch.com>
Date: Thu, 5 Sep 2024 14:40:45 -0400
Subject: [PATCH 4/8] archive

---
 R/{ => archive}/dataset_metadata.R |  0
 R/date_time_conversions.R          | 65 ------------------------------
 2 files changed, 65 deletions(-)
 rename R/{ => archive}/dataset_metadata.R (100%)
 delete mode 100644 R/date_time_conversions.R

diff --git a/R/dataset_metadata.R b/R/archive/dataset_metadata.R
similarity index 100%
rename from R/dataset_metadata.R
rename to R/archive/dataset_metadata.R
diff --git a/R/date_time_conversions.R b/R/date_time_conversions.R
deleted file mode 100644
index 9097c0c..0000000
--- a/R/date_time_conversions.R
+++ /dev/null
@@ -1,65 +0,0 @@
-# This file contains several helpers for reading and writing date / datetime
-# columns from a Dataset JSON file
-
-#' Get the column classes off a data frame
-#'
-#' @param x A data.frame
-#'
-#' @return Named character vector of columns and types
-#' @noRd
-get_column_classes <- function(x) {
-  vapply(x, function(X) class(X)[1], FUN.VALUE=character(1))
-}
-
-#' Get the columns with a class of Date from a data.frame
-#'
-#' @param x A data.frame
-#'
-#' @return A data.frame
-#' @noRd
-get_date_cols <- function(x) {
-  x[get_column_classes(x) == "Date"]
-}
-
-#' Get the columns with a class of POSIXct from a data.frame
-#'
-#' @param x A data.frame
-#'
-#' @return A data.frame
-#' @noRd
-get_datetime_cols <- function(x) {
-  x[get_column_classes(x) == "POSIXct"]
-}
-
-#' Convert a Date object in R to a SAS date origin
-#'
-#' R uses POSIX date origins, and SAS uses a date origin of 1960-01-01, so to
-#' convert you need to add 10 years (plus three leap year days) in days
-#'
-#' @param x A data.frame
-#'
-#' @return A data.frame
-#' @noRd
-convert_to_sas_datenum <- function(x) {
-  col_names <- names(get_date_cols(x))
-  # Add 10 years in days (including 3 leap year days)
-  x[col_names] <- lapply(get_date_cols(x) + (365 * 10) + 3, as.numeric)
-  x
-}
-
-#' Convert a POSIXct object in R to a SAS date origin
-#'
-#' R uses POSIX date origins, and SAS uses a date origin of 1960-01-01, so to
-#' convert you need to add 10 years (plus three leap year days) in seconds
-#'
-#' @param x A data.frame
-#'
-#' @return A data.frame
-#' @noRd
-convert_to_sas_datetimenum <- function(x) {
-  col_names <- names(get_datetime_cols(x))
-  # Add 10 years in seconds (including 3 leap year days)
-  x[col_names] <- lapply(get_datetime_cols(x) + (365 * 24 * 60 * 60 * 10) + (3 * 24 * 60 * 60), as.numeric)
-
-  x
-}

From 70f4aa3f6a03056769110167a39b8eeb51606741 Mon Sep 17 00:00:00 2001
From: mstackhouse <Mike.Stackhouse@atorusresearch.com>
Date: Thu, 5 Sep 2024 14:41:11 -0400
Subject: [PATCH 5/8] Update docs

---
 NAMESPACE                                |  17 +---
 data-raw/data.R                          |  73 ----------------
 data/iris_items.rda                      | Bin 334 -> 334 bytes
 man/data_metadata.Rd                     |  36 --------
 man/data_metadata_setters.Rd             |  38 ---------
 man/dataset_json.Rd                      | 101 +++++++++++------------
 man/dataset_metadata.Rd                  |  34 --------
 man/dataset_metadata_setters.Rd          |  91 ++++++++++++++++++++
 man/file_metadata.Rd                     |  51 ------------
 man/file_metadata_setters.Rd             |  61 --------------
 man/sas_date_formats.Rd                  |  22 -----
 man/sas_datetime_formats.Rd              |  22 -----
 man/sas_time_formats.Rd                  |  22 -----
 man/{schema_1_0_0.Rd => schema_1_1_0.Rd} |  12 +--
 man/set_as_reference_data.Rd             |  21 +++++
 15 files changed, 170 insertions(+), 431 deletions(-)
 delete mode 100644 man/data_metadata.Rd
 delete mode 100644 man/data_metadata_setters.Rd
 delete mode 100644 man/dataset_metadata.Rd
 create mode 100644 man/dataset_metadata_setters.Rd
 delete mode 100644 man/file_metadata.Rd
 delete mode 100644 man/file_metadata_setters.Rd
 delete mode 100644 man/sas_date_formats.Rd
 delete mode 100644 man/sas_datetime_formats.Rd
 delete mode 100644 man/sas_time_formats.Rd
 rename man/{schema_1_0_0.Rd => schema_1_1_0.Rd} (64%)
 create mode 100644 man/set_as_reference_data.Rd

diff --git a/NAMESPACE b/NAMESPACE
index a9a5cd9..5a563e6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,21 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(set_metadata_ref,data_metadata)
-S3method(set_metadata_ref,datasetjson)
-S3method(set_metadata_ref,default)
-S3method(set_metadata_version,data_metadata)
-S3method(set_metadata_version,datasetjson)
-S3method(set_metadata_version,default)
-S3method(set_study_oid,data_metadata)
-S3method(set_study_oid,datasetjson)
-S3method(set_study_oid,default)
-export(data_metadata)
 export(dataset_json)
-export(dataset_metadata)
-export(file_metadata)
 export(read_dataset_json)
-export(set_data_type)
+export(set_as_reference_data)
+export(set_dataset_label)
+export(set_dataset_name)
 export(set_file_oid)
+export(set_item_oid)
 export(set_metadata_ref)
 export(set_metadata_version)
 export(set_originator)
diff --git a/data-raw/data.R b/data-raw/data.R
index 1444d4c..5a737e4 100644
--- a/data-raw/data.R
+++ b/data-raw/data.R
@@ -64,79 +64,6 @@ iris_items_bad <- tibble::tribble(
   NA_character_,        5,     'Flower Species',   'character', 10L,           1,
 )
 
-# Code for SAS date formats
-sas_date_formats <- c(
-  'DATE.',
-  'DATE9.',
-  'DAY.',
-  'DDMMYY.',
-  'DDMMYY10.',
-  'DDMMYYB.',
-  'DDMMYYB10.',
-  'DDMMYYC.',
-  'DDMMYYC10.',
-  'DDMMYYD.',
-  'DDMMYYD10.',
-  'DDMMYYN6.',
-  'DDMMYYN8.',
-  'DDMMYYP.',
-  'DDMMYYP10.',
-  'DDMMYYS.',
-  'DDMMYYS10.',
-  'DOWNAME.',
-  'JULIAN.',
-  'MMDDYY.',
-  'MMDDYY10.',
-  'MMDDYYB.',
-  'MMDDYYB10.',
-  'MMDDYYC.',
-  'MMDDYYC10.',
-  'MMDDYYD.',
-  'MMDDYYD10.',
-  'MMDDYYN6.',
-  'MMDDYYN8.',
-  'MMDDYYP.',
-  'MMDDYYP10.',
-  'MMDDYYS.',
-  'MMDDYYS10.',
-  'MMYY.',
-  'MMYYC.',
-  'MMYYD.',
-  'MMYYN.',
-  'MMYYP.',
-  'MMYYS.',
-  'MONNAME.',
-  'MONTH.',
-  'MONYY.',
-  'WEEKDATE.',
-  'WEEKDATX',
-  'WEEKDAY.'
-)
-
-usethis::use_data(sas_date_formats, overwrite = TRUE)
-
-# Code for SAS datetime formats
-sas_datetime_formats <- c(
-  'DATEAMPM.',
-  'DATETIME.',
-  'DTDATE.',
-  'DTMONYY.',
-  'DTWKDATX.',
-  'DTYEAR.',
-  'DTYYQC.'
-)
-
-usethis::use_data(sas_datetime_formats, overwrite = TRUE)
-
-# Code for SAS time formats
-sas_time_formats <- c(
-  'HOUR.',
-  'TIME.',
-  'TIMEAMPM.',
-  'TOD.'
-)
-usethis::use_data(sas_time_formats, overwrite = TRUE)
-
 # Dataset JSON Schema V1.0.0 as Character Vector
 schema_file <- testthat::test_path("testdata", "dataset.schema.json")
 schema_1_1_0 = readChar(schema_file, file.info(schema_file)$size)
diff --git a/data/iris_items.rda b/data/iris_items.rda
index f26da5cc54480104d0ef497de4ebf258d6a87fd7..c817b7bcade4b4c19ef7e04458e7bc780fc49fa3 100644
GIT binary patch
delta 316
zcmV-C0mJ^z0?q;sLRx4!F+o`-Q&~9eJY$g#9e*?>6*L}+lT8?z01W^DJqR?^(wNi@
zr~ow4pglkU8VL~+o|=K628}c{9w-1bX{l>P17?cd%)4dGnM5TGa7-1jAtUNBl{p%D
zP%I=VWQc;H52htRfC)$e+-B<}zY)q<?v04BD9Z*XaB(pskU%gI3?Ld&Y)ewmfnyzV
z34d1OQ!zsf5W~;<>+7dqjtIW?`*5Ks_&}=-bQCqEtTm&ZV?b1bbx(GT%s)W{l1k3h
zvq)3<%&aZYn;`i!L~G<A+qL}&RB9y*c@?5n96>x_K!Q{xNi>SdG-8rqMS<K@`3j$4
zJL3b+O47_0+Y&7~mWejF@@V_5j5;c1-X&t7ye6E#fYWL#Bdzi0pu6wVOJcVLKo%rF
Oi@744C`cT3o-u$5(1CRT

delta 316
zcmV-C0mJ^z0?q;sLRx4!F+o`-Q&~+CxKWV~9e*fEN@zVzG8!>700007p$3|oLrI9x
z13{xeXaE{C5+sOE)iMBKFqoP=P}58%nK-U!pgL$*I=e3uWTc2n8t;@8+6YMB7D-E?
zsY-z&Q(GJoLV@xnt_28)1U$2Lg4IanEQ_mOECPmF7@Wh!i5J8J0T99gr4a!Q2o;f@
zK!23xab<{MS{QwDomA=P@meaWzgp;ROHCzMV?je&TEi3*tOyE_PPy+<ormZkl1Vt~
zRc8tRJ&~n-t6V=OaGe2g9crJUaf6cD*V7y-BZx4@1SnJrB{Ym|nea(4CPQZg{z8Zv
z7JOcP=~$G&Im}R+rb*OCf*Jk1`2#D$TP0*8LT*;#_yIylEsmH6--g$}N?Me>F#yPs
O{9VZu;X*+)O5sE}c75Ie

diff --git a/man/data_metadata.Rd b/man/data_metadata.Rd
deleted file mode 100644
index 9786158..0000000
--- a/man/data_metadata.Rd
+++ /dev/null
@@ -1,36 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_metadata.R
-\name{data_metadata}
-\alias{data_metadata}
-\title{Create the data metadata container for a Dataset JSON object}
-\usage{
-data_metadata(study = NULL, metadata_version = NULL, metadata_ref = NULL)
-}
-\arguments{
-\item{study}{Study OID value}
-
-\item{metadata_version}{Metadata version OID value}
-
-\item{metadata_ref}{Metadata reference (i.e. path to Define.xml)}
-}
-\value{
-data_metadata object
-}
-\description{
-Create the data metadata container for a Dataset JSON object
-}
-\examples{
-# Create object directly
-data_meta <- data_metadata(
-  study = "SOMESTUDY",
-  metadata_version = "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7",
-  metadata_ref = "some/define.xml"
-)
-
-# Use setter functions
-data_meta <- data_metadata()
-data_meta_updated <- set_metadata_ref(data_meta, "some/define.xml")
-data_meta_updated <- set_metadata_version(data_meta_updated, "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7")
-data_meta_updated <- set_study_oid(data_meta_updated, "SOMESTUDY")
-
-}
diff --git a/man/data_metadata_setters.Rd b/man/data_metadata_setters.Rd
deleted file mode 100644
index f02fe01..0000000
--- a/man/data_metadata_setters.Rd
+++ /dev/null
@@ -1,38 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_metadata.R
-\name{set_study_oid}
-\alias{set_study_oid}
-\alias{set_metadata_version}
-\alias{set_metadata_ref}
-\title{Set data metadata parameters}
-\usage{
-set_study_oid(x, study, ...)
-
-set_metadata_version(x, metadata_version, ...)
-
-set_metadata_ref(x, metadata_ref)
-}
-\arguments{
-\item{x}{data metadata or datasetjson object}
-
-\item{study}{Study OID value}
-
-\item{...}{Additional parameters}
-
-\item{metadata_version}{Metadata version OID value}
-
-\item{metadata_ref}{Metadata reference (i.e. path to Define.xml)}
-}
-\value{
-A datasetjson or data_metadata object
-}
-\description{
-This set of functions
-}
-\examples{
-data_meta <- data_metadata()
-data_meta_updated <- set_metadata_ref(data_meta, "some/define.xml")
-data_meta_updated <- set_metadata_version(data_meta_updated, "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7")
-data_meta_updated <- set_study_oid(data_meta_updated, "SOMESTUDY")
-}
-\concept{Data metadata setters}
diff --git a/man/dataset_json.Rd b/man/dataset_json.Rd
index c84ffc6..cd9f37d 100644
--- a/man/dataset_json.Rd
+++ b/man/dataset_json.Rd
@@ -6,45 +6,47 @@
 \usage{
 dataset_json(
   .data,
-  item_id,
-  name,
-  label,
-  items,
-  dataset_meta,
-  version = "1.0.0",
-  data_type = c("clinicalData", "referenceData"),
-  file_meta = file_metadata(),
-  data_meta = data_metadata()
+  file_oid = NULL,
+  originator = NULL,
+  sys = NULL,
+  sys_version = NULL,
+  study = NULL,
+  metadata_version = NULL,
+  metadata_ref = NULL,
+  item_oid = NULL,
+  name = NULL,
+  dataset_label = NULL,
+  version = "1.1.0"
 )
 }
 \arguments{
 \item{.data}{Input data to contain within the Dataset JSON file. Written to
 the itemData parameter.}
 
-\item{item_id}{ID used to label dataset with the itemGroupData parameter.
-Defined as "Object of Datasets. Key value is a unique identifier for
-Dataset, corresponding to ItemGroupDef/@OID in Define-XML."}
+\item{file_oid}{fileOID parameter, defined as "A unique identifier for this
+file."}
 
-\item{name}{Dataset name}
+\item{originator}{originator parameter, defined as "The organization that
+generated the Dataset-JSON file."}
 
-\item{label}{Dataset Label}
+\item{sys}{sourceSystem parameter, defined as "The computer system or
+database management system that is the source of the information in this
+file."}
 
-\item{items}{Variable metadata}
+\item{sys_version}{sourceSystemVersion, defined as "The version of the
+sourceSystem"}
 
-\item{dataset_meta}{A dataset_metadata object holding pre-specified
-dataset metadata.}
+\item{study}{Study OID value}
 
-\item{version}{Version of Dataset JSON schema to follow.}
+\item{metadata_version}{Metadata version OID value}
 
-\item{data_type}{Type of data being written. clinicalData for subject level
-data, and referenceData for non-subject level data (i.e. TDMs, Associated
-Persons)}
+\item{metadata_ref}{Metadata reference (i.e. path to Define.xml)}
 
-\item{file_meta}{A file_metadata object holding pre-specified file
-metadata}
+\item{item_oid}{ID used to label dataset with the itemGroupData parameter.
+Defined as "Object of Datasets. Key value is a unique identifier for
+Dataset, corresponding to ItemGroupDef/@OID in Define-XML."}
 
-\item{data_meta}{A data_metadata object holding pre-specified data
-metadata}
+\item{version}{The DatasetJSON version to use. Currently only 1.1.0 is supported.}
 }
 \value{
 dataset_json object pertaining to the specific Dataset JSON version
@@ -53,9 +55,26 @@ specific
 \description{
 Create the base object used to write a Dataset JSON file.
 }
+\details{
+Note that DatasetJSON is on version 1.1.0. Based off findings from the pilot,
+version 1.1.0 reflects feedback from the user community. Support for 1.0.0 has
+been deprecated.
+}
 \examples{
 # Create a basic object
-ds_json <- dataset_json(iris, "IG.IRIS", "IRIS", "Iris", iris_items)
+ds_json <- dataset_json(
+  iris, 
+  file_oid = "/some/path"
+  originator = "Some Org", 
+  sys = "source system", 
+  sys_version = "1.0", 
+  study = "SOMESTUDY",
+  metadata_version = "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7",
+  metadata_ref = "some/define.xml",
+  item_oid = "IG.IRIS",
+  name = "IRIS",
+  dataset_label = "Iris"
+)
 
 # Attach attributes directly
 ds_json_updated <- set_data_type(ds_json, "referenceData")
@@ -65,31 +84,7 @@ ds_json_updated <- set_metadata_version(ds_json_updated, "MDV.MSGv2.0.SDTMIG.3.3
 ds_json_updated <- set_originator(ds_json_updated, "Some Org")
 ds_json_updated <- set_source_system(ds_json_updated, "source system", "1.0")
 ds_json_updated <- set_study_oid(ds_json_updated, "SOMESTUDY")
-
-# Create independent objects for metadata sections first
-file_meta <- file_metadata(
-  originator = "Some Org",
-  sys = "source system",
-  sys_version = "1.0"
-)
-
-data_meta <- data_metadata(
-  study = "SOMESTUDY",
-  metadata_version = "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7",
-  metadata_ref = "some/define.xml"
-)
-
-dataset_meta <- dataset_metadata(
-  item_id = "IG.IRIS",
-  name = "IRIS",
-  label = "Iris",
-  items = iris_items
-)
-
-ds_json_from_meta <- dataset_json(
-  iris,
-  dataset_meta = dataset_meta,
-  file_meta = file_meta,
-  data_meta = data_meta
-  )
+ds_json_updated <- set_item_oid(ds_json_updated, "IG.IRIS")
+ds_json_updated <- set_dataset_name(ds_json_updated, "IRIS")
+ds_json_updated <- set_dataseT_label(ds_json_updated, "Iris")
 }
diff --git a/man/dataset_metadata.Rd b/man/dataset_metadata.Rd
deleted file mode 100644
index 9dea9fc..0000000
--- a/man/dataset_metadata.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/dataset_metadata.R
-\name{dataset_metadata}
-\alias{dataset_metadata}
-\title{Generate an individual element that fills the itemGroupData field}
-\usage{
-dataset_metadata(item_id, name, label, items, .data)
-}
-\arguments{
-\item{item_id}{Data Object ID for item in Dataset JSON object, corresponding to
-ItemGroupDef/@OID in Define-XML.}
-
-\item{name}{Dataset name}
-
-\item{label}{Dataset Label}
-
-\item{items}{Variable metadata}
-
-\item{.data}{Dataframe to be written to Dataset JSON file}
-}
-\value{
-dataset_metadata object
-}
-\description{
-Generate an individual element that fills the itemGroupData field
-}
-\examples{
-dataset_meta <- dataset_metadata(
-  item_id = "IG.IRIS",
-  name = "IRIS",
-  label = "Iris",
-  items = iris_items
-)
-}
diff --git a/man/dataset_metadata_setters.Rd b/man/dataset_metadata_setters.Rd
new file mode 100644
index 0000000..dcbab0a
--- /dev/null
+++ b/man/dataset_metadata_setters.Rd
@@ -0,0 +1,91 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/file_metadata.R
+\name{set_source_system}
+\alias{set_source_system}
+\alias{set_originator}
+\alias{set_file_oid}
+\alias{set_study_oid}
+\alias{set_metadata_version}
+\alias{set_metadata_ref}
+\alias{set_item_oid}
+\alias{set_dataset_name}
+\alias{set_dataset_label}
+\title{Dataset Metadata Setters}
+\usage{
+set_source_system(x, sys, sys_version)
+
+set_originator(x, originator)
+
+set_file_oid(x, file_oid)
+
+set_study_oid(x, study)
+
+set_metadata_version(x, metadata_version)
+
+set_metadata_ref(x, metadata_ref)
+
+set_item_oid(x, item_oid)
+
+set_dataset_name(x, name)
+
+set_dataset_label(x, dataset_label)
+}
+\arguments{
+\item{x}{datasetjson object}
+
+\item{sys}{sourceSystem parameter, defined as "The computer system or
+database management system that is the source of the information in this
+file."}
+
+\item{sys_version}{sourceSystemVersion, defined as "The version of the
+sourceSystem"}
+
+\item{originator}{originator parameter, defined as "The organization that
+generated the Dataset-JSON file."}
+
+\item{file_oid}{fileOID parameter, defined as "A unique identifier for this
+file."}
+
+\item{study}{Study OID value}
+
+\item{metadata_version}{Metadata version OID value}
+
+\item{metadata_ref}{Metadata reference (i.e. path to Define.xml)}
+
+\item{item_oid}{ID used to label dataset with the itemGroupData parameter.
+Defined as "Object of Datasets. Key value is a unique identifier for
+Dataset, corresponding to ItemGroupDef/@OID in Define-XML."}
+
+\item{name}{Dataset name}
+
+\item{dataset_label}{Dataset Label}
+}
+\value{
+datasetjson object
+}
+\description{
+Set information about the file, source system, study, and dataset used to generate the Dataset
+JSON object.
+}
+\details{
+The fileOID parameter should be structured following description outlined in
+the ODM V2.0 specification. "FileOIDs should be universally unique if at all
+possible. One way to ensure this is to prefix every FileOID with an internet
+domain name owned by the creator of the ODM file or database (followed by a
+forward slash, "/"). For example,
+FileOID="BestPharmaceuticals.com/Study5894/1" might be a good way to denote
+the first file in a series for study 5894 from Best Pharmaceuticals."
+}
+\examples{
+ds_json <- dataset_json(iris)
+ds_json <- set_file_oid(ds_json, "/some/path")
+ds_json <- set_study_oid(ds_json, "SOMESTUDY")
+ds_json <- set_originator(ds_json, "Some Org")
+ds_json <- set_source_system(ds_json, "source system", "1.0")
+ds_json <- set_metadata_ref(ds_json, "some/define.xml")
+ds_json <- set_metadata_version(ds_json, "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7")
+ds_json <- set_item_oid(ds_json, "IG.IRIS")
+ds_json <- set_dataset_name(ds_json, "IRIS")
+ds_json <- set_dataset_label(ds_json, "Iris")
+}
+\concept{Dataset Metadata Setters}
diff --git a/man/file_metadata.Rd b/man/file_metadata.Rd
deleted file mode 100644
index 342285d..0000000
--- a/man/file_metadata.Rd
+++ /dev/null
@@ -1,51 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/file_metadata.R
-\name{file_metadata}
-\alias{file_metadata}
-\title{Create a file metadata object}
-\usage{
-file_metadata(
-  originator = NULL,
-  sys = NULL,
-  sys_version = NULL,
-  file_oid = NULL,
-  version = "1.0.0"
-)
-}
-\arguments{
-\item{originator}{originator parameter, defined as "The organization that
-generated the Dataset-JSON file."}
-
-\item{sys}{sourceSystem parameter, defined as "The computer system or
-database management system that is the source of the information in this
-file."}
-
-\item{sys_version}{sourceSystemVersion, defined as "The version of the
-sourceSystem"}
-
-\item{file_oid}{fileOID parameter, defined as "A unique identifier for this
-file."}
-
-\item{version}{Dataset JSON schema version being used}
-}
-\value{
-file_metadata object
-}
-\description{
-Create a file metadata object
-}
-\examples{
-# Create using parameters
-file_meta <- file_metadata(
-    originator = "Some Org",
-    sys = "source system",
-    sys_version = "1.0"
-  )
-
-# Set parameters after
-file_meta <- file_metadata()
-
-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")
-}
diff --git a/man/file_metadata_setters.Rd b/man/file_metadata_setters.Rd
deleted file mode 100644
index 4b5dd0f..0000000
--- a/man/file_metadata_setters.Rd
+++ /dev/null
@@ -1,61 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/file_metadata.R
-\name{set_source_system}
-\alias{set_source_system}
-\alias{set_originator}
-\alias{set_file_oid}
-\alias{set_data_type}
-\title{File Metadata Setters}
-\usage{
-set_source_system(x, sys, sys_version)
-
-set_originator(x, originator)
-
-set_file_oid(x, file_oid)
-
-set_data_type(x, data_type = c("clinicalData", "referenceData"))
-}
-\arguments{
-\item{x}{datasetjson object}
-
-\item{sys}{sourceSystem parameter, defined as "The computer system or
-database management system that is the source of the information in this
-file."}
-
-\item{sys_version}{sourceSystemVersion, defined as "The version of the
-sourceSystem"}
-
-\item{originator}{originator parameter, defined as "The organization that
-generated the Dataset-JSON file."}
-
-\item{file_oid}{fileOID parameter, defined as "A unique identifier for this
-file."}
-
-\item{data_type}{Type of data being written. clinicalData for subject level
-data, and referenceData for non-subject level data (i.e. TDMs, Associated
-Persons)}
-}
-\value{
-datasetjson or file_metadata object
-}
-\description{
-Set information about the file and source system used to generate the Dataset
-JSON object.
-}
-\details{
-The fileOID parameter should be structured following description outlined in
-the ODM V2.0 specification. "FileOIDs should be universally unique if at all
-possible. One way to ensure this is to prefix every FileOID with an internet
-domain name owned by the creator of the ODM file or database (followed by a
-forward slash, "/"). For example,
-FileOID="BestPharmaceuticals.com/Study5894/1" might be a good way to denote
-the first file in a series for study 5894 from Best Pharmaceuticals."
-}
-\examples{
-file_meta <- file_metadata()
-
-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")
-}
-\concept{File Metadata Setters}
diff --git a/man/sas_date_formats.Rd b/man/sas_date_formats.Rd
deleted file mode 100644
index ebf3449..0000000
--- a/man/sas_date_formats.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data.R
-\docType{data}
-\name{sas_date_formats}
-\alias{sas_date_formats}
-\title{A List of valid SAS(c) date formats}
-\format{
-\subsection{\code{sas_date_formats}}{
-
-\describe{
-A character vector with 45 elements
-}
-}
-}
-\usage{
-sas_date_formats
-}
-\description{
-Valid SAS(c) date formats pulled from
-https://documentation.sas.com/doc/en/vdmmlcdc/8.1/ds2pg/p0bz5detpfj01qn1kz2in7xymkdl.htm
-}
-\keyword{datasets}
diff --git a/man/sas_datetime_formats.Rd b/man/sas_datetime_formats.Rd
deleted file mode 100644
index d8358a6..0000000
--- a/man/sas_datetime_formats.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data.R
-\docType{data}
-\name{sas_datetime_formats}
-\alias{sas_datetime_formats}
-\title{A List of valid SAS(c) datetime formats}
-\format{
-\subsection{\code{sas_datetime_formats}}{
-
-\describe{
-A character vector with 7 elements
-}
-}
-}
-\usage{
-sas_datetime_formats
-}
-\description{
-Valid SAS(c) datetime formats pulled from
-https://documentation.sas.com/doc/en/vdmmlcdc/8.1/ds2pg/p0bz5detpfj01qn1kz2in7xymkdl.htm
-}
-\keyword{datasets}
diff --git a/man/sas_time_formats.Rd b/man/sas_time_formats.Rd
deleted file mode 100644
index 60588f4..0000000
--- a/man/sas_time_formats.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data.R
-\docType{data}
-\name{sas_time_formats}
-\alias{sas_time_formats}
-\title{A List of valid SAS(c) time formats}
-\format{
-\subsection{\code{sas_time_formats}}{
-
-\describe{
-A character vector with 4 elements
-}
-}
-}
-\usage{
-sas_time_formats
-}
-\description{
-Valid SAS(c) time formats pulled from
-https://documentation.sas.com/doc/en/vdmmlcdc/8.1/ds2pg/p0bz5detpfj01qn1kz2in7xymkdl.htm
-}
-\keyword{datasets}
diff --git a/man/schema_1_0_0.Rd b/man/schema_1_1_0.Rd
similarity index 64%
rename from man/schema_1_0_0.Rd
rename to man/schema_1_1_0.Rd
index 633c00b..189a927 100644
--- a/man/schema_1_0_0.Rd
+++ b/man/schema_1_1_0.Rd
@@ -1,11 +1,11 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/data.R
 \docType{data}
-\name{schema_1_0_0}
-\alias{schema_1_0_0}
-\title{Dataset JSON Schema Version 1.0.0}
+\name{schema_1_1_0}
+\alias{schema_1_1_0}
+\title{Dataset JSON Schema Version 1.1.0}
 \format{
-\subsection{\code{schema_1_0_0}}{
+\subsection{\code{schema_1_1_0}}{
 
 \describe{
 A character vector with 1 element
@@ -13,9 +13,9 @@ A character vector with 1 element
 }
 }
 \usage{
-schema_1_0_0
+schema_1_1_0
 }
 \description{
-This object is a character vector holding the schema for Dataset JSON Version 1.0.0
+This object is a character vector holding the schema for Dataset JSON Version 1.1.0
 }
 \keyword{datasets}
diff --git a/man/set_as_reference_data.Rd b/man/set_as_reference_data.Rd
new file mode 100644
index 0000000..173bd93
--- /dev/null
+++ b/man/set_as_reference_data.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/file_metadata.R
+\name{set_as_reference_data}
+\alias{set_as_reference_data}
+\title{Declare as reference data}
+\usage{
+set_as_reference_data(x)
+}
+\arguments{
+\item{x}{datasetjson object}
+}
+\value{
+datasetjson object
+}
+\description{
+Sets DatasetJSON file to have the isReferenceData attribute set to TRUE
+}
+\examples{
+ds_json <- dataset_json(iris)
+ds_json <- set_as_reference_data(ds_json)
+}

From 836b803a9adfebc162cf728400705221b389b186 Mon Sep 17 00:00:00 2001
From: Michael Stackhouse <michaelstackhouse0614@gmail.com>
Date: Thu, 5 Sep 2024 15:47:00 -0400
Subject: [PATCH 6/8] Update R/datasetjson.R

Co-authored-by: Nicholas Masel <61123199+nicholas-masel@users.noreply.github.com>
---
 R/datasetjson.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/datasetjson.R b/R/datasetjson.R
index 840eed0..f3279ba 100644
--- a/R/datasetjson.R
+++ b/R/datasetjson.R
@@ -57,7 +57,7 @@
 #' ds_json_updated <- set_study_oid(ds_json_updated, "SOMESTUDY")
 #' ds_json_updated <- set_item_oid(ds_json_updated, "IG.IRIS")
 #' ds_json_updated <- set_dataset_name(ds_json_updated, "IRIS")
-#' ds_json_updated <- set_dataseT_label(ds_json_updated, "Iris")
+#' ds_json_updated <- set_dataset_label(ds_json_updated, "Iris")
 dataset_json <- function(.data, file_oid = NULL, originator=NULL, sys=NULL, 
                           sys_version = NULL, study=NULL, metadata_version=NULL,
                           metadata_ref=NULL, item_oid=NULL, name=NULL, 

From 6de009cdcf0b4d71daca76a2e6beb7f0967d9251 Mon Sep 17 00:00:00 2001
From: mstackhouse <Mike.Stackhouse@atorusresearch.com>
Date: Thu, 5 Sep 2024 16:48:30 -0400
Subject: [PATCH 7/8] Updates from discussion

---
 NAMESPACE                                     |  2 +-
 R/datasetjson.R                               | 18 +++++----
 R/file_metadata.R                             | 40 +++++++++++++++++--
 man/dataset_json.Rd                           |  6 ++-
 man/dataset_metadata_setters.Rd               |  3 ++
 ...eference_data.Rd => set_reference_data.Rd} |  6 +--
 6 files changed, 60 insertions(+), 15 deletions(-)
 rename man/{set_as_reference_data.Rd => set_reference_data.Rd} (81%)

diff --git a/NAMESPACE b/NAMESPACE
index 5a563e6..ccbacf6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,7 +2,6 @@
 
 export(dataset_json)
 export(read_dataset_json)
-export(set_as_reference_data)
 export(set_dataset_label)
 export(set_dataset_name)
 export(set_file_oid)
@@ -10,6 +9,7 @@ export(set_item_oid)
 export(set_metadata_ref)
 export(set_metadata_version)
 export(set_originator)
+export(set_reference_data)
 export(set_source_system)
 export(set_study_oid)
 export(validate_dataset_json)
diff --git a/R/datasetjson.R b/R/datasetjson.R
index f3279ba..906a5b5 100644
--- a/R/datasetjson.R
+++ b/R/datasetjson.R
@@ -25,6 +25,8 @@
 #' @param item_oid ID used to label dataset with the itemGroupData parameter.
 #'   Defined as "Object of Datasets. Key value is a unique identifier for
 #'   Dataset, corresponding to ItemGroupDef/@OID in Define-XML."
+#' @param ref_data Boolean value that is set to "true" when the dataset contains 
+#'   reference data (not subject data). The default value is "false". 
 #' @param version The DatasetJSON version to use. Currently only 1.1.0 is supported.
 #'
 #' @return dataset_json object pertaining to the specific Dataset JSON version
@@ -61,9 +63,9 @@
 dataset_json <- function(.data, file_oid = NULL, originator=NULL, sys=NULL, 
                           sys_version = NULL, study=NULL, metadata_version=NULL,
                           metadata_ref=NULL, item_oid=NULL, name=NULL, 
-                          dataset_label=NULL, version="1.1.0") {
+                          dataset_label=NULL, ref_data=FALSE, version="1.1.0") {
   new_dataset_json(.data, file_oid, originator, sys, sys_version, study, metadata_version,
-                   metadata_ref, item_oid, name, dataset_label, version)
+                   metadata_ref, item_oid, name, dataset_label, ref_data, version)
 }
 
 #' Create a base Dataset JSON Container
@@ -77,7 +79,7 @@ dataset_json <- function(.data, file_oid = NULL, originator=NULL, sys=NULL,
 #' @noRd
 new_dataset_json <- function(.data, file_oid, originator, sys, sys_version, study, 
                              metadata_version, metadata_ref, item_oid, name, dataset_label,
-                             version) {
+                             ref_data, version) {
 
   if (!(version %in% c("1.1.0"))) {
     stop("Unsupported version specified - currently only version 1.1.0 is supported", call.=FALSE)
@@ -90,7 +92,8 @@ new_dataset_json <- function(.data, file_oid, originator, sys, sys_version, stud
 
   # Extract the function and call it to return the base structure
   funcs[[version]](.data, file_oid, originator, sys, sys_version, study, 
-                   metadata_version, metadata_ref, item_oid, name, dataset_label)
+                   metadata_version, metadata_ref, item_oid, name, dataset_label,
+                   ref_data)
 }
 
 #' Dataset JSON v1.1.0 Generator
@@ -98,7 +101,8 @@ new_dataset_json <- function(.data, file_oid, originator, sys, sys_version, stud
 #' @return datasetjson_v1_1_0 object
 #' @noRd
 new_dataset_json_v1_1_0 <- function(.data, file_oid, originator, sys, sys_version, study, 
-                                    metadata_version, metadata_ref, item_oid, name, dataset_label) {
+                                    metadata_version, metadata_ref, item_oid, name, dataset_label, 
+                                    ref_data) {
 
   if (!inherits(.data, 'data.frame')) {
     stop("datasetjson objects must inherit from a data.frame", call.=FALSE)
@@ -111,16 +115,16 @@ new_dataset_json_v1_1_0 <- function(.data, file_oid, originator, sys, sys_versio
     )
   }
 
+  attr(.data, 'datasetJSONVersion') <- "1.1.0"
   attr(.data, 'fileOID') <- file_oid
   attr(.data, 'originator') <- originator
   attr(.data, 'studyOID') <- study
   attr(.data, 'metaDataVersionOID') <- metadata_version
   attr(.data, 'metaDataRef') <- metadata_ref
   attr(.data, "itemGroupOID") <- item_oid
-  attr(.data, 'records') <- nrow(x)
   attr(.data, 'name') <- name
   attr(.data, 'label') <- dataset_label
-  attr(.data, 'isReferenceData') <- FALSE
+  attr(.data, 'isReferenceData') <- ref_data
   
   structure(
     .data,
diff --git a/R/file_metadata.R b/R/file_metadata.R
index e0ca4cd..cf5f15f 100644
--- a/R/file_metadata.R
+++ b/R/file_metadata.R
@@ -29,6 +29,8 @@
 #' @param item_oid ID used to label dataset with the itemGroupData parameter.
 #'   Defined as "Object of Datasets. Key value is a unique identifier for
 #'   Dataset, corresponding to ItemGroupDef/@OID in Define-XML."
+#' @param ref_data Boolean value that is set to "true" when the dataset contains 
+#'   reference data (not subject data). The default value is "false". 
 #' @param name Dataset name
 #' @param dataset_label Dataset Label
 #'
@@ -50,6 +52,12 @@
 #' ds_json <- set_dataset_label(ds_json, "Iris")
 set_source_system <- function(x, sys, sys_version) {
   stopifnot_datasetjson(x)
+  if (!is.character(sys)) {
+    stop("`sys` must be a character")
+  }
+  if (!is.character(sys_version)) {
+    stop("`sys_version` must be a character")
+  }
   attr(x, 'sourceSystem') <- list(
     "name" = sys,
     "version" = sys_version
@@ -62,6 +70,9 @@ set_source_system <- function(x, sys, sys_version) {
 #' @rdname dataset_metadata_setters
 set_originator <- function(x, originator) {
   stopifnot_datasetjson(x)
+  if (!is.character(originator)) {
+    stop("`originator` must be a character")
+  }
   attr(x, 'originator') <- originator
   x
 }
@@ -71,6 +82,9 @@ set_originator <- function(x, originator) {
 #' @rdname dataset_metadata_setters
 set_file_oid <- function(x, file_oid) {
   stopifnot_datasetjson(x)
+  if (!is.character(file_oid)) {
+    stop("`file_oid` must be a character")
+  }
   attr(x, 'fileOID') <- file_oid
   x
 }
@@ -80,6 +94,9 @@ set_file_oid <- function(x, file_oid) {
 #' @rdname dataset_metadata_setters
 set_study_oid <- function(x, study) {
   stopifnot_datasetjson(x)
+  if (!is.character(study)) {
+    stop("`study` must be a character")
+  }
   attr(x, 'studyOID') <- study
   x
 }
@@ -89,6 +106,9 @@ set_study_oid <- function(x, study) {
 #' @rdname dataset_metadata_setters
 set_metadata_version <- function(x, metadata_version) {
   stopifnot_datasetjson(x)
+  if (!is.character(metadata_version)) {
+    stop("`metadata_version` must be a character")
+  }
   attr(x, 'metaDataVersionOID') <- metadata_version
   x
 }
@@ -98,6 +118,9 @@ set_metadata_version <- function(x, metadata_version) {
 #' @rdname dataset_metadata_setters
 set_metadata_ref <- function(x, metadata_ref) {
   stopifnot_datasetjson(x)
+  if (!is.character(metadata_ref)) {
+    stop("`metadata_ref` must be a character")
+  }
   attr(x, 'metaDataRef') <- metadata_ref
   x
 }
@@ -107,6 +130,9 @@ set_metadata_ref <- function(x, metadata_ref) {
 #' @rdname dataset_metadata_setters
 set_item_oid <- function(x, item_oid) {
   stopifnot_datasetjson(x)
+  if (!is.character(item_oid)) {
+    stop("`item_oid` must be a character")
+  }
   attr(x, "itemGroupOID") <- item_oid
 }
 
@@ -115,6 +141,9 @@ set_item_oid <- function(x, item_oid) {
 #' @rdname dataset_metadata_setters
 set_dataset_name <- function(x, name) {
   stopifnot_datasetjson(x)
+  if (!is.character(name)) {
+    stop("`name` must be a character")
+  }
   attr(x, 'name') <- name
 }
 
@@ -123,6 +152,9 @@ set_dataset_name <- function(x, name) {
 #' @rdname dataset_metadata_setters
 set_dataset_label <- function(x, dataset_label) {
   stopifnot_datasetjson(x)
+  if (!is.character(dataset_labelx)) {
+    stop("`dataset_label` must be a character")
+  }
   attr(x, 'label') <- dataset_label
 }
 
@@ -138,12 +170,14 @@ set_dataset_label <- function(x, dataset_label) {
 #' @examples
 #' ds_json <- dataset_json(iris)
 #' ds_json <- set_as_reference_data(ds_json)
-set_as_reference_data <- function(x) {
+set_reference_data <- function(x, is_refdata) {
   stopifnot_datasetjson(x)
-  attr(x, 'isReferenceData') <- TRUE
+  if (!is.logical(is_refdata)) {
+    stop("`is_refdata` must be a boolean")
+  }
+  attr(x, 'isReferenceData') <- is_refdata
 }
 
-
 #' Create an ISO8601 formatted datetime of the current time
 #'
 #' This is used to create the creationDateTime and asOfDateTime attributes of
diff --git a/man/dataset_json.Rd b/man/dataset_json.Rd
index cd9f37d..d538d80 100644
--- a/man/dataset_json.Rd
+++ b/man/dataset_json.Rd
@@ -16,6 +16,7 @@ dataset_json(
   item_oid = NULL,
   name = NULL,
   dataset_label = NULL,
+  ref_data = FALSE,
   version = "1.1.0"
 )
 }
@@ -46,6 +47,9 @@ sourceSystem"}
 Defined as "Object of Datasets. Key value is a unique identifier for
 Dataset, corresponding to ItemGroupDef/@OID in Define-XML."}
 
+\item{ref_data}{Boolean value that is set to "true" when the dataset contains
+reference data (not subject data). The default value is "false".}
+
 \item{version}{The DatasetJSON version to use. Currently only 1.1.0 is supported.}
 }
 \value{
@@ -86,5 +90,5 @@ ds_json_updated <- set_source_system(ds_json_updated, "source system", "1.0")
 ds_json_updated <- set_study_oid(ds_json_updated, "SOMESTUDY")
 ds_json_updated <- set_item_oid(ds_json_updated, "IG.IRIS")
 ds_json_updated <- set_dataset_name(ds_json_updated, "IRIS")
-ds_json_updated <- set_dataseT_label(ds_json_updated, "Iris")
+ds_json_updated <- set_dataset_label(ds_json_updated, "Iris")
 }
diff --git a/man/dataset_metadata_setters.Rd b/man/dataset_metadata_setters.Rd
index dcbab0a..c0c2caf 100644
--- a/man/dataset_metadata_setters.Rd
+++ b/man/dataset_metadata_setters.Rd
@@ -59,6 +59,9 @@ Dataset, corresponding to ItemGroupDef/@OID in Define-XML."}
 \item{name}{Dataset name}
 
 \item{dataset_label}{Dataset Label}
+
+\item{ref_data}{Boolean value that is set to "true" when the dataset contains
+reference data (not subject data). The default value is "false".}
 }
 \value{
 datasetjson object
diff --git a/man/set_as_reference_data.Rd b/man/set_reference_data.Rd
similarity index 81%
rename from man/set_as_reference_data.Rd
rename to man/set_reference_data.Rd
index 173bd93..e52a644 100644
--- a/man/set_as_reference_data.Rd
+++ b/man/set_reference_data.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/file_metadata.R
-\name{set_as_reference_data}
-\alias{set_as_reference_data}
+\name{set_reference_data}
+\alias{set_reference_data}
 \title{Declare as reference data}
 \usage{
-set_as_reference_data(x)
+set_reference_data(x, is_refdata)
 }
 \arguments{
 \item{x}{datasetjson object}

From 7d4f4bae7f368f951c868abbe2c7b7cb1c1a136e Mon Sep 17 00:00:00 2001
From: mstackhouse <Mike.Stackhouse@atorusresearch.com>
Date: Thu, 5 Sep 2024 16:56:42 -0400
Subject: [PATCH 8/8] docs and cleanup

---
 NAMESPACE                       |  1 +
 R/datasetjson.R                 | 29 +++++++++++++++++------------
 R/file_metadata.R               | 24 +++++++++++++-----------
 man/dataset_json.Rd             |  5 ++++-
 man/dataset_metadata_setters.Rd |  6 ++++++
 man/set_reference_data.Rd       | 21 ---------------------
 6 files changed, 41 insertions(+), 45 deletions(-)
 delete mode 100644 man/set_reference_data.Rd

diff --git a/NAMESPACE b/NAMESPACE
index ccbacf6..03d40e1 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -6,6 +6,7 @@ export(set_dataset_label)
 export(set_dataset_name)
 export(set_file_oid)
 export(set_item_oid)
+export(set_last_modified)
 export(set_metadata_ref)
 export(set_metadata_version)
 export(set_originator)
diff --git a/R/datasetjson.R b/R/datasetjson.R
index 906a5b5..ec453cc 100644
--- a/R/datasetjson.R
+++ b/R/datasetjson.R
@@ -37,7 +37,8 @@
 #' # Create a basic object
 #' ds_json <- dataset_json(
 #'   iris, 
-#'   file_oid = "/some/path"
+#'   file_oid = "/some/path",
+#'   last_modified = "2023-02-15T10:23:15",
 #'   originator = "Some Org", 
 #'   sys = "source system", 
 #'   sys_version = "1.0", 
@@ -52,6 +53,7 @@
 #' # Attach attributes directly
 #' ds_json_updated <- set_data_type(ds_json, "referenceData")
 #' ds_json_updated <- set_file_oid(ds_json_updated, "/some/path")
+#' ds_json_updates <- set_last_modified(ds_json_updates, "2023-02-15T10:23:15")
 #' ds_json_updated <- set_metadata_ref(ds_json_updated, "some/define.xml")
 #' ds_json_updated <- set_metadata_version(ds_json_updated, "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7")
 #' ds_json_updated <- set_originator(ds_json_updated, "Some Org")
@@ -60,12 +62,14 @@
 #' ds_json_updated <- set_item_oid(ds_json_updated, "IG.IRIS")
 #' ds_json_updated <- set_dataset_name(ds_json_updated, "IRIS")
 #' ds_json_updated <- set_dataset_label(ds_json_updated, "Iris")
-dataset_json <- function(.data, file_oid = NULL, originator=NULL, sys=NULL, 
-                          sys_version = NULL, study=NULL, metadata_version=NULL,
-                          metadata_ref=NULL, item_oid=NULL, name=NULL, 
-                          dataset_label=NULL, ref_data=FALSE, version="1.1.0") {
-  new_dataset_json(.data, file_oid, originator, sys, sys_version, study, metadata_version,
-                   metadata_ref, item_oid, name, dataset_label, ref_data, version)
+dataset_json <- function(.data, file_oid = NULL, last_modified=NULL, 
+                          originator=NULL, sys=NULL, sys_version = NULL, 
+                          study=NULL, metadata_version=NULL,metadata_ref=NULL, 
+                          item_oid=NULL, name=NULL, dataset_label=NULL, ref_data=FALSE, 
+                          version="1.1.0") {
+  new_dataset_json(.data, file_oid, last_modified, originator, sys, sys_version, study, 
+                   metadata_version, metadata_ref, item_oid, name, dataset_label, ref_data, 
+                   version)
 }
 
 #' Create a base Dataset JSON Container
@@ -77,7 +81,7 @@ dataset_json <- function(.data, file_oid = NULL, originator=NULL, sys=NULL,
 #' @return datasetjson object
 #'
 #' @noRd
-new_dataset_json <- function(.data, file_oid, originator, sys, sys_version, study, 
+new_dataset_json <- function(.data, file_oid, last_modified, originator, sys, sys_version, study, 
                              metadata_version, metadata_ref, item_oid, name, dataset_label,
                              ref_data, version) {
 
@@ -91,7 +95,7 @@ new_dataset_json <- function(.data, file_oid, originator, sys, sys_version, stud
   )
 
   # Extract the function and call it to return the base structure
-  funcs[[version]](.data, file_oid, originator, sys, sys_version, study, 
+  funcs[[version]](.data, file_oid, last_modified, originator, sys, sys_version, study, 
                    metadata_version, metadata_ref, item_oid, name, dataset_label,
                    ref_data)
 }
@@ -100,9 +104,9 @@ new_dataset_json <- function(.data, file_oid, originator, sys, sys_version, stud
 #'
 #' @return datasetjson_v1_1_0 object
 #' @noRd
-new_dataset_json_v1_1_0 <- function(.data, file_oid, originator, sys, sys_version, study, 
-                                    metadata_version, metadata_ref, item_oid, name, dataset_label, 
-                                    ref_data) {
+new_dataset_json_v1_1_0 <- function(.data, file_oid, last_modified, originator, sys, sys_version, 
+                                    study, metadata_version, metadata_ref, item_oid, name, 
+                                    dataset_label, ref_data) {
 
   if (!inherits(.data, 'data.frame')) {
     stop("datasetjson objects must inherit from a data.frame", call.=FALSE)
@@ -117,6 +121,7 @@ new_dataset_json_v1_1_0 <- function(.data, file_oid, originator, sys, sys_versio
 
   attr(.data, 'datasetJSONVersion') <- "1.1.0"
   attr(.data, 'fileOID') <- file_oid
+  attr(.data, 'dbLastModifiedDateTime') <- last_modified
   attr(.data, 'originator') <- originator
   attr(.data, 'studyOID') <- study
   attr(.data, 'metaDataVersionOID') <- metadata_version
diff --git a/R/file_metadata.R b/R/file_metadata.R
index cf5f15f..738b382 100644
--- a/R/file_metadata.R
+++ b/R/file_metadata.R
@@ -158,18 +158,9 @@ set_dataset_label <- function(x, dataset_label) {
   attr(x, 'label') <- dataset_label
 }
 
-#' Declare as reference data
-#' 
-#' Sets DatasetJSON file to have the isReferenceData attribute set to TRUE
-#' 
-#' @param x datasetjson object
-#' 
-#' @return datasetjson object
 #' @export
-#' 
-#' @examples
-#' ds_json <- dataset_json(iris)
-#' ds_json <- set_as_reference_data(ds_json)
+#' @family Dataset Metadata Setters
+#' @rdname dataset_metadata_setters
 set_reference_data <- function(x, is_refdata) {
   stopifnot_datasetjson(x)
   if (!is.logical(is_refdata)) {
@@ -178,6 +169,17 @@ set_reference_data <- function(x, is_refdata) {
   attr(x, 'isReferenceData') <- is_refdata
 }
 
+#' @export
+#' @family Dataset Metadata Setters
+#' @rdname dataset_metadata_setters
+set_last_modified <- function(x, last_modified) {
+  stopifnot_datasetjson(x)
+  if (!is.character(last_modified)) {
+    stop("`last_modified` must be a character")
+  }
+  attr(x, 'dbLastModifiedDateTime') <- last_modified
+}
+
 #' Create an ISO8601 formatted datetime of the current time
 #'
 #' This is used to create the creationDateTime and asOfDateTime attributes of
diff --git a/man/dataset_json.Rd b/man/dataset_json.Rd
index d538d80..91f6532 100644
--- a/man/dataset_json.Rd
+++ b/man/dataset_json.Rd
@@ -7,6 +7,7 @@
 dataset_json(
   .data,
   file_oid = NULL,
+  last_modified = NULL,
   originator = NULL,
   sys = NULL,
   sys_version = NULL,
@@ -68,7 +69,8 @@ been deprecated.
 # Create a basic object
 ds_json <- dataset_json(
   iris, 
-  file_oid = "/some/path"
+  file_oid = "/some/path",
+  last_modified = "2023-02-15T10:23:15",
   originator = "Some Org", 
   sys = "source system", 
   sys_version = "1.0", 
@@ -83,6 +85,7 @@ ds_json <- dataset_json(
 # Attach attributes directly
 ds_json_updated <- set_data_type(ds_json, "referenceData")
 ds_json_updated <- set_file_oid(ds_json_updated, "/some/path")
+ds_json_updates <- set_last_modified(ds_json_updates, "2023-02-15T10:23:15")
 ds_json_updated <- set_metadata_ref(ds_json_updated, "some/define.xml")
 ds_json_updated <- set_metadata_version(ds_json_updated, "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7")
 ds_json_updated <- set_originator(ds_json_updated, "Some Org")
diff --git a/man/dataset_metadata_setters.Rd b/man/dataset_metadata_setters.Rd
index c0c2caf..900f055 100644
--- a/man/dataset_metadata_setters.Rd
+++ b/man/dataset_metadata_setters.Rd
@@ -10,6 +10,8 @@
 \alias{set_item_oid}
 \alias{set_dataset_name}
 \alias{set_dataset_label}
+\alias{set_reference_data}
+\alias{set_last_modified}
 \title{Dataset Metadata Setters}
 \usage{
 set_source_system(x, sys, sys_version)
@@ -29,6 +31,10 @@ set_item_oid(x, item_oid)
 set_dataset_name(x, name)
 
 set_dataset_label(x, dataset_label)
+
+set_reference_data(x, is_refdata)
+
+set_last_modified(x, last_modified)
 }
 \arguments{
 \item{x}{datasetjson object}
diff --git a/man/set_reference_data.Rd b/man/set_reference_data.Rd
deleted file mode 100644
index e52a644..0000000
--- a/man/set_reference_data.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/file_metadata.R
-\name{set_reference_data}
-\alias{set_reference_data}
-\title{Declare as reference data}
-\usage{
-set_reference_data(x, is_refdata)
-}
-\arguments{
-\item{x}{datasetjson object}
-}
-\value{
-datasetjson object
-}
-\description{
-Sets DatasetJSON file to have the isReferenceData attribute set to TRUE
-}
-\examples{
-ds_json <- dataset_json(iris)
-ds_json <- set_as_reference_data(ds_json)
-}