Merge pull request #45 from atorus-research/gh_issue_43

Gh issue 43

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)

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")

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"]
+}

R/data.R

@@ -15,45 +15,12 @@
 #' }
 "iris_items"
 
-#' A List of valid SAS(c) date formats
+#' Dataset JSON Schema Version 1.1.0
 #'
-#' Valid SAS(c) date formats pulled from
-#' https://documentation.sas.com/doc/en/vdmmlcdc/8.1/ds2pg/p0bz5detpfj01qn1kz2in7xymkdl.htm
+#' This object is a character vector holding the schema for Dataset JSON Version 1.1.0
 #'
-#' @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 1.0.0
-#'
-#' This object is a character vector holding the schema for Dataset JSON Version 1.0.0
-#'
-#' @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"