Merge pull request #19 from atorus-research/github_issue_3_16

GitHub issue #3,  #16, #17, #18, #20

DESCRIPTION

@@ -24,8 +24,8 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Depends: R (>= 3.5)
 Imports:
-    jsonlite (>= 1.8.7),
-    jsonvalidate (>= 1.3.2)
+    jsonlite (>= 1.8.0),
+    jsonvalidate (>= 1.3.1)
 Suggests:
     testthat (>= 2.1.0),
     knitr,

NEWS.md

@@ -1,6 +1,10 @@
 # datasetjson 0.0.1.9000
 
 - Capability to read and validate Dataset JSON files from URLs has been added (#8)
+- Remove autoset of fileOID using output path (#3)
+- Don't auto-populate optional attributes with NA (#16)
+- Push dependency versions back (#18)
+- Default `pretty` parameter on `write_dataset_json()` to false (#20)
 
 # datasetjson 0.0.1
 

R/data_metadata.R

@@ -21,7 +21,7 @@
 #' 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 = "NA", metadata_version = "NA", metadata_ref = "NA") {
+data_metadata <- function(study = NULL, metadata_version = NULL, metadata_ref = NULL) {
 
   x <- list(
     studyOID = study,

R/file_metadata.R

@@ -7,6 +7,8 @@
 #'   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
@@ -26,17 +28,17 @@
 #' file_meta_updated <- set_file_oid(file_meta, "/some/path")
 #' file_meta_updated <- set_originator(file_meta_updated, "Some Org")
 #' file_meta_updated <- set_source_system(file_meta_updated, "source system", "1.0")
-file_metadata <- function(originator="NA", sys = "NA", sys_version = "NA", version = "1.0.0") {
+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"= get_datetime(),
+    "creationDateTime"= character(),
     "datasetJSONVersion"= version,
-    "fileOID" = character(),
-    "asOfDateTime" = character(),
+    "fileOID" = file_oid,
+    "asOfDateTime" = NULL, # Not sure we want this to exist?
     "originator" = originator,
     "sourceSystem" = sys,
     "sourceSystemVersion" = sys_version
@@ -59,10 +61,20 @@ get_datetime <- function() {
   format(Sys.time(), "%Y-%m-%dT%H:%M:%S")
 }
 
-#' Set source system information
+#' File Metadata Setters
+#'
+#' Set information about the file and source system used to generate the Dataset
+#' JSON object.
+#'
+#' @details
 #'
-#' Set information about the source system used to generate the Dataset JSON
-#' object.
+#' 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."
 #'
 #' @param x datasetjson object
 #' @param sys sourceSystem parameter, defined as "The computer system or

R/utils.R

@@ -55,6 +55,41 @@ set_col_attr <- function(nm, d, attr, items) {
   x
 }
 
+#' Get the index of nulls in a list
+#'
+#' @param x A list
+#'
+#' @return Integer vector of indices
+#' @noRd
+get_null_inds <- function(x) {
+  which(vapply(x, is.null, FUN.VALUE = TRUE))
+}
+
+#' Remove nulls from a Dataset JSON object
+#'
+#' Only targets the file and data metadata to pull off optional elements
+#'
+#' @param x A Dataset JSON object
+#'
+#' @return A Dataset JSON object
+#' @noRd
+remove_nulls <- function(x) {
+
+  # Specifically target the data metadata
+  dm_nulls <- get_null_inds(x[[get_data_type(x)]])
+  if (length(dm_nulls) > 0) {
+    x[[get_data_type(x)]] <- x[[get_data_type(x)]][-dm_nulls]
+  }
+
+  # Top level
+  fm_nulls <- get_null_inds(x)
+  if (length(fm_nulls) > 0) {
+    x <- x[-fm_nulls]
+  }
+
+  x
+}
+
 #' Check if given path is a URL
 #'
 #' @param path character string

R/write_dataset_json.R

@@ -16,22 +16,19 @@
 #' \dontrun{
 #'   write_dataset_json(ds_json, "path/to/file.json")
 #' }
-write_dataset_json <- function(x, file, pretty=TRUE) {
+write_dataset_json <- function(x, file, pretty=FALSE) {
   stopifnot_datasetjson(x)
 
-  # Populate the as-of datetime
-  x[['asOfDateTime']] <- get_datetime()
+  # Populate the creation datetime
+  x[['creationDateTime']] <- get_datetime()
+
+  x <- remove_nulls(x)
 
   if (!missing(file)) {
     # Make sure the output path exists
     if(!dir.exists(dirname(file))) {
       stop("Folder supplied to `file` does not exist", call.=FALSE)
     }
-
-    # Attach the file OID
-    x <- set_file_oid(x, tools::file_path_sans_ext(file))
-  } else{
-    x <- set_file_oid(x, "NA")
   }
 
   # Create the JSON text

README.Rmd

@@ -7,11 +7,7 @@ knitr::opts_chunk$set(echo = TRUE)
 library(datasetjson)
 ```
 
-# datasetjson
-
-<!-- Please do not edit the README.md file as it is auto-generated after PR merges. Only edit the README.Rmd file -->
-<!-- The purpose of this is to enable dynamic links using dyn_link function above to access devel/main admiral homepage respectively -->
-<!-- To test this in your feature branch use code: rmarkdown::render("README.Rmd", output_format ="md_document") -->
+# **datasetjson** <img src="man/figures/logo.svg" align="right" alt="" width="120" />
 
 <!-- badges: start -->
 [<img src="https://img.shields.io/codecov/c/github/atorus-research/datasetjson">](https://app.codecov.io/gh/atorus-research/datasetjson)
@@ -67,7 +63,7 @@ write_dataset_json(ds_updated, file = "./iris.json")
 Or if you don't provide a file path, the JSON text will return directly. 
 
 ```{r write_print}
-js_text <- write_dataset_json(ds_updated)
+js_text <- write_dataset_json(ds_updated, pretty=TRUE)
 cat(js_text)
 ```
 
@@ -87,6 +83,8 @@ print(attr(dat$Sepal.Width, "type"))
 ```
 Note that Dataset JSON is an early CDISC standard and is still subject to change, as as such this package will be updated. Backwards compatibility will be enforced once the standard itself is more stable. Until then, it is not recommended to use this package within production activities. 
 
+# [<img src="man/figures/cdisc.png" alt="" width="120" />](https://www.cdisc.org/)
+
 ## Acknowledgements
 
 Thank you to Ben Straub and Eric Simms (GSK) for help and input during the original CDISC Dataset JSON hackathon that motivated this work.

README.md

@@ -1,9 +1,6 @@
 
-# datasetjson
+# **datasetjson** <img src="man/figures/logo.svg" align="right" alt="" width="120" />
 
-<!-- Please do not edit the README.md file as it is auto-generated after PR merges. Only edit the README.Rmd file -->
-<!-- The purpose of this is to enable dynamic links using dyn_link function above to access devel/main admiral homepage respectively -->
-<!-- To test this in your feature branch use code: rmarkdown::render("README.Rmd", output_format ="md_document") -->
 <!-- badges: start -->
 
 [<img src="https://img.shields.io/codecov/c/github/atorus-research/datasetjson">](https://app.codecov.io/gh/atorus-research/datasetjson)
@@ -73,15 +70,14 @@ write_dataset_json(ds_updated, file = "./iris.json")
 Or if you don’t provide a file path, the JSON text will return directly.
 
 ``` r
-js_text <- write_dataset_json(ds_updated)
+js_text <- write_dataset_json(ds_updated, pretty=TRUE)
 cat(js_text)
 ```
 
     ## {
-    ##   "creationDateTime": "2023-09-15T17:57:31",
+    ##   "creationDateTime": "2023-09-25T12:20:23",
     ##   "datasetJSONVersion": "1.0.0",
-    ##   "fileOID": "NA",
-    ##   "asOfDateTime": "2023-09-15T17:57:31",
+    ##   "fileOID": "/some/path",
     ##   "originator": "Some Org",
     ##   "sourceSystem": "source system",
     ##   "sourceSystemVersion": "1.0",
@@ -174,7 +170,7 @@ attached as attributes on the data frame itself:
 print(attr(dat, "creationDateTime"))
 ```
 
-    ## [1] "2023-09-15T17:57:31"
+    ## [1] "2023-09-25T12:20:23"
 
 ``` r
 print(attr(dat$Sepal.Length, "OID"))
@@ -194,6 +190,8 @@ compatibility will be enforced once the standard itself is more stable.
 Until then, it is not recommended to use this package within production
 activities.
 
+# [<img src="man/figures/cdisc.png" alt="" width="120" />](https://www.cdisc.org/)
+
 ## Acknowledgements
 
 Thank you to Ben Straub and Eric Simms (GSK) for help and input during

tests/testthat/test-data_metadata.R

@@ -1,9 +1,9 @@
 data_meta <- data_metadata()
 
 test_that("Default data_metadata object produces correctly", {
-  expect_equal(data_meta$studyOID, "NA")
-  expect_equal(data_meta$metaDataVersionOID, "NA")
-  expect_equal(data_meta$metaDataRef, "NA")
+  expect_null(data_meta$studyOID)
+  expect_null(data_meta$metaDataVersionOID)
+  expect_null(data_meta$metaDataRef)
 })
 
 test_that("data_metadata setters work properly", {

tests/testthat/test-datasetjson.R

@@ -8,23 +8,23 @@ test_that("datasetjson object builds with minimal defaults", {
 
   # I just want to remove the potential for a corner case
   # where the call to system time splits across a second
-  expect_equal(grep("\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}", ds_json$creationDateTime), 1)
+  # expect_equal(grep("\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}", ds_json$creationDateTime), 1)
 
   # File metadata
   expect_equal(ds_json$datasetJSONVersion, "1.0.0")
-  expect_equal(ds_json$fileOID, character())
-  expect_equal(ds_json$asOfDateTime, character())
-  expect_equal(ds_json$originator, "NA")
-  expect_equal(ds_json$sourceSystem, "NA")
-  expect_equal(ds_json$sourceSystemVersion, "NA")
+  expect_null(ds_json$fileOID)
+  expect_null(ds_json$asOfDateTime)
+  expect_null(ds_json$originator)
+  expect_null(ds_json$sourceSystem)
+  expect_null(ds_json$sourceSystemVersion)
 
   # Data type is correct
   expect_equal(tail(names(ds_json), 1), "clinicalData")
 
   # Data metadata
-  expect_equal(ds_json$clinicalData$studyOID, "NA")
-  expect_equal(ds_json$clinicalData$metaDataVersionOID, "NA")
-  expect_equal(ds_json$clinicalData$metaDataRef, "NA")
+  expect_null(ds_json$clinicalData$studyOID)
+  expect_null(ds_json$clinicalData$metaDataVersionOID)
+  expect_null(ds_json$clinicalData$metaDataRef)
 
   # item_id passes through
   expect_equal(names(ds_json$clinicalData$itemGroupData), "IG.IRIS")

tests/testthat/test-file_metadata.R

@@ -2,11 +2,11 @@ test_that("Default file_metadata object produces correctly", {
   file_meta <- file_metadata()
 
   expect_equal(file_meta$datasetJSONVersion, "1.0.0")
-  expect_equal(file_meta$fileOID, character())
-  expect_equal(file_meta$asOfDateTime, character())
-  expect_equal(file_meta$originator, "NA")
-  expect_equal(file_meta$sourceSystem, "NA")
-  expect_equal(file_meta$sourceSystemVersion, "NA")
+  expect_null(file_meta$fileOID, character())
+  expect_null(file_meta$asOfDateTime)
+  expect_null(file_meta$originator)
+  expect_null(file_meta$sourceSystem)
+  expect_null(file_meta$sourceSystemVersion)
 })
 
 test_that("Parameters pass through on file_metadata call", {