Merge pull request #47 from atorus-research/gh_issue_43

Updates from discussion
atorus-research · Sep 5, 2024 · 2cca514 · 2cca514
2 parents 2dc4c43 + 7d4f4ba
commit 2cca514
Show file tree

Hide file tree

Showing 6 changed files with 93 additions and 52 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -2,14 +2,15 @@
 
 export(dataset_json)
 export(read_dataset_json)
-export(set_as_reference_data)
 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)
+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
@@ -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
@@ -35,7 +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", 
@@ -50,6 +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")
@@ -58,12 +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, 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)
+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
@@ -75,9 +81,9 @@ 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,
-                             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)
@@ -89,16 +95,18 @@ 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)
+  funcs[[version]](.data, file_oid, last_modified, originator, sys, sys_version, study, 
+                   metadata_version, metadata_ref, item_oid, name, dataset_label,
+                   ref_data)
 }
 
 #' Dataset JSON v1.1.0 Generator
 #'
 #' @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) {
+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)
@@ -111,16 +119,17 @@ 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
   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
@@ -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
 }
 
@@ -123,26 +152,33 @@ 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
 }
 
-#' 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) {
+#' @family Dataset Metadata Setters
+#' @rdname dataset_metadata_setters
+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
 }
 
+#' @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
 #'

diff --git a/man/dataset_json.Rd b/man/dataset_json.Rd
diff --git a/man/dataset_metadata_setters.Rd b/man/dataset_metadata_setters.Rd
diff --git a/man/set_as_reference_data.Rd b/man/set_as_reference_data.Rd