Type:	Package
Title:	Read and Write CDISC Dataset JSON Files
Version:	0.3.0
Description:	Read, construct and write CDISC (Clinical Data Interchange Standards Consortium) Dataset JSON (JavaScript Object Notation) files, while validating per the Dataset JSON schema file, as described in CDISC (2023) https://www.cdisc.org/standards/data-exchange/dataset-json.
URL:	https://atorus-research.github.io/datasetjson/
BugReports:	https://github.com/atorus-research/datasetjson/issues/
Encoding:	UTF-8
Language:	en-US
License:	Apache License (≥ 2)
LazyData:	true
RoxygenNote:	7.3.2
Depends:	R (≥ 4.0)
Imports:	yyjsonr (≥ 0.1.18), jsonvalidate (≥ 1.3.1), hms
Suggests:	testthat (≥ 2.1.0), jsonlite (≥ 1.8.0), knitr, haven, rmarkdown, withr, purrr, tibble, dplyr, lubridate, data.table
VignetteBuilder:	knitr
Config/testthat/edition:	3
NeedsCompilation:	no
Packaged:	2025-01-30 15:44:49 UTC; mstackhouse
Author:	Mike Stackhouse [aut, cre], Nicholas Masel [aut]
Maintainer:	Mike Stackhouse <mike.stackhouse@atorusresearch.com>
Repository:	CRAN
Date/Publication:	2025-01-30 16:00:01 UTC

datasetjson: Read and Write CDISC Dataset JSON Files

Description

Read, construct and write CDISC (Clinical Data Interchange Standards Consortium) Dataset JSON (JavaScript Object Notation) files, while validating per the Dataset JSON schema file, as described in CDISC (2023) https://www.cdisc.org/standards/data-exchange/dataset-json.

Author(s)

Maintainer: Mike Stackhouse mike.stackhouse@atorusresearch.com (ORCID)

Authors:

• Nicholas Masel nmasel@its.jnj.com

See Also

Useful links:

• https://atorus-research.github.io/datasetjson/

• Report bugs at https://github.com/atorus-research/datasetjson/issues/

Create a Dataset JSON Object

Description

Create the base object used to write a Dataset JSON file.

Usage

dataset_json(
  .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,
  columns = NULL,
  version = "1.1.0"
)

Arguments

Details

The columns parameter should be provided as a dataframe based off the Dataset JSON Specification:

• itemOID: string, required: Unique identifier for the variable that may also function as a foreign key to an ItemDef/@OID in an associated Define-XML file. See the ODM specification for OID considerations.

• name: string, required: Variable name

• label: string, required: Variable label

• dataType: string, required: Logical data type of the variable. The dataType attribute represents the planned specificity of the data. See the ODM Data Formats specification for details. -targetDataType: string, optional: Indicates the data type into which the receiving system must transform the associated Dataset-JSON variable. The variable with the data type attribute of dataType must be converted into the targetDataType when transforming the Dataset-JSON dataset into a format for operational use (e.g., SAS dataset, R dataframe, loading into a system's data store). Only specify targetDataType when it is different from the dataType attribute or the JSON data type and the data needs to be transformed by the receiving system. See the Supported Column Data Type Combinations table for details on usage. See the User's Guide for additional information.

• length: integer, optional: Specifies the number of characters allowed for the variable value when it is represented as a text.

• displayFormat: *string, optional: A SAS display format value used for data visualization of numeric float and date values.

• keySequence: integer, optional: Indicates that this item is a key variable in the dataset structure. It also provides an ordering for the keys.

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.

Value

dataset_json object pertaining to the specific Dataset JSON version specific

Examples

# Create a basic object
ds_json <- dataset_json(
  iris,
  file_oid = "/some/path",
  last_modified = "2023-02-15T10:23:15",
  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",
  columns = iris_items
)

# Attach attributes directly
ds_json <- dataset_json(iris, columns = iris_items)
ds_json <- set_file_oid(ds_json, "/some/path")
ds_json <- set_last_modified(ds_json, "2025-01-21T13:34:50")
ds_json <- set_originator(ds_json, "Some Org")
ds_json <- set_source_system(ds_json, "source system", "1.0")
ds_json <- set_study_oid(ds_json, "SOMESTUDY")
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, "The Iris Dataset")

Extract column metadata to data frame

Description

This function pulls out the column metadata from the datasetjson object attributes into a more user-friendly data.frame.

Usage

get_column_metadata(x)

Arguments

Value

A data frame containing the columns metadata

Examples

ds_json <- dataset_json(
  iris,
  item_oid = "IG.IRIS",
  name = "IRIS",
  dataset_label = "Iris",
  columns = iris_items
)

get_column_metadata(ds_json)

Example Variable Metadata for Iris

Description

Example of the necessary variable metadata included in a Dataset JSON file based on the Iris data frame.

Usage

iris_items

Format

iris_items A data frame with 5 rows and 6 columns:

itemOID

Unique identifier for Variable. Must correspond to ItemDef/@OID in Define-XML.

name

Display format supports data visualization of numeric float and date values.

label

Label for Variable

dataType

Data type for Variable

length

Length for Variable

keySequence

Indicates that this item is a key variable in the dataset structure. It also provides an ordering for the keys.

Read a Dataset JSON to datasetjson object

Description

This function validates a dataset JSON file against the Dataset JSON schema, and if valid returns a datasetjson object. The Dataset JSON file can be either a file path on disk of a URL which contains the Dataset JSON file.

Usage

read_dataset_json(file, decimals_as_floats = FALSE)

Arguments

Details

The resulting dataframe contains the additional metadata available on the Dataset JSON file within the attributes to make this accessible to the user. Note that these attributes are only populated if available.

• sourceSystem: The information system from which the content of this dataset was source, including system name and version.

• datasetJSONVersion: The version of the Dataset-JSON standard used to create the dataset.

• fileOID: A unique identifier for this dataset.

• dbLastModifiedDateTime: The date/time the source database was last modified before creating the Dataset-JSON file.

• originator: The organization that generated the Dataset-JSON dataset.

• studyOID: Unique identifier for the study that may also function as a foreign key to a Study/@OID in an associated Define-XML document, or to any studyOID references that are used as keys in other documents;

• metaDataVersionOID: Unique identifier for the metadata version that may also function as a foreign key to a MetaDataVersion/@OID in an associated Define-XML file

• metaDataRef: URI for the metadata file describing the dataset (e.g., a Define-XML file).

• itemGroupOID: Unique identifier for the dataset that may also function as a foreign key to an ItemGroupDef/@OID in an associated Define-XML file.

• name: The human-readable name for the dataset.

• label: A short description of the dataset.

• columns: An array of metadata objects that describe the dataset variables. See dataset_json() for further information on the contents of these fields.

Value

A dataframe with additional attributes attached containing the DatasetJSON metadata.

Examples

# Read from disk
## Not run: 
  dat <- read_dataset_json("path/to/file.json")
 # Read file from URL
  dat <- dataset_json('https://www.somesite.com/file.json')

## End(Not run)

# Read from an already imported character vector
ds_json <- dataset_json(iris, "IG.IRIS", "IRIS", "Iris", columns=iris_items)
js <- write_dataset_json(ds_json)
dat <- read_dataset_json(js)

Dataset JSON Schema Version 1.1.0

Description

This object is a character vector holding the schema for Dataset JSON Version 1.1.0

Usage

schema_1_1_0

Format

schema_1_1_0

A character vector with 1 element

Dataset Metadata Setters

Description

Set information about the file, source system, study, and dataset used to generate the Dataset JSON object.

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)

set_last_modified(x, last_modified)

Arguments

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."

Value

datasetjson object

Examples

ds_json <- dataset_json(iris, columns = iris_items)
ds_json <- set_file_oid(ds_json, "/some/path")
ds_json <- set_last_modified(ds_json, "2025-01-21T13:34:50")
ds_json <- set_originator(ds_json, "Some Org")
ds_json <- set_source_system(ds_json, "source system", "1.0")
ds_json <- set_study_oid(ds_json, "SOMESTUDY")
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, "The Iris Dataset")

Assign Dataset JSON attributes to data frame columns

Description

Using the columns element of the Dataset JSON file, assign the available metadata to individual columns

Usage

set_variable_attributes(x)

Arguments

Value

A datasetjson object with attributes assigned to individual variables

Examples

ds_json <- dataset_json(
  iris,
  item_oid = "IG.IRIS",
  name = "IRIS",
  dataset_label = "Iris",
  columns = iris_items
)

ds_json <- set_variable_attributes(ds_json)

Validate a Dataset JSON file

Description

This function calls jsonvalidate::json_validate() directly, with the parameters necessary to retrieve the error information of an invalid JSON file per the Dataset JSON schema.

Usage

validate_dataset_json(x)

Arguments

Value

A data frame

Examples

## Not run: 
  validate_dataset_json('path/to/file.json')
  validate_dataset_json('https://www.somesite.com/file.json')

## End(Not run)

ds_json <- dataset_json(
  iris,
  item_oid = "IG.IRIS",
  name = "IRIS",
  dataset_label = "Iris",
  columns = iris_items
)
js <- write_dataset_json(ds_json)

validate_dataset_json(js)

Write out a Dataset JSON file

Description

Write out a Dataset JSON file

Usage

write_dataset_json(
  x,
  file,
  pretty = FALSE,
  float_as_decimals = FALSE,
  digits = 16
)

Arguments

Value

NULL when file written to disk, otherwise character string

Examples

# Write to character object
ds_json <- dataset_json(
  iris,
  item_oid = "IG.IRIS",
  name = "IRIS",
  dataset_label = "Iris",
  columns = iris_items
)
js <- write_dataset_json(ds_json)

# Write to disk
## Not run: 
  write_dataset_json(ds_json, "path/to/file.json")

## End(Not run)