Package 'datasetjson'

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

.data	Input data to contain within the Dataset JSON file. Written to the itemData parameter.
file_oid	fileOID parameter, defined as "A unique identifier for this file." (optional)
last_modified	The date/time the source database was last modified before creating the Dataset-JSON file (optional)
originator	originator parameter, defined as "The organization that generated the Dataset-JSON file." (optional)
sys	sourceSystem.name parameter, defined as "The computer system or database management system that is the source of the information in this file." (Optional, required if coupled with sys_version)
sys_version	sourceSystem.Version, defined as "The version of the sourceSystem" (Optional, required if coupled with sys)
study	Study OID value (optional)
metadata_version	Metadata version OID value (optional)
metadata_ref	Metadata reference (i.e. path to Define.xml) (optional)
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."
name	Dataset name
dataset_label	Dataset Label
columns	Variable level metadata for the Dataset JSON object. See details for format requirements.
version	The DatasetJSON version to use. Currently only 1.1.0 is supported.

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

x	A datasetjson object

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

file	File path or URL of a Dataset JSON file
decimals_as_floats	Convert variables of "decimal" type to float

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

x	datasetjson object
sys	sourceSystem.name parameter, defined as "The computer system or database management system that is the source of the information in this file." (Optional, required if coupled with sys_version)
sys_version	sourceSystem.Version, defined as "The version of the sourceSystem" (Optional, required if coupled with sys)
originator	originator parameter, defined as "The organization that generated the Dataset-JSON file." (optional)
file_oid	fileOID parameter, defined as "A unique identifier for this file." (optional)
study	Study OID value (optional)
metadata_version	Metadata version OID value (optional)
metadata_ref	Metadata reference (i.e. path to Define.xml) (optional)
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."
name	Dataset name
dataset_label	Dataset Label
last_modified	The date/time the source database was last modified before creating the Dataset-JSON file (optional)

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

x	A datasetjson object

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

x	File path or URL of a Dataset JSON file, or a character vector holding JSON text

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

x	datasetjson object
file	File path to save Dataset JSON file
pretty	If TRUE, write with readable formatting. Note: The Dataset JSON standard prefers compressed formatting without line feeds. It is not recommended you use pretty printing for submission purposes.
float_as_decimals	If TRUE, Convert float variables to "decimal" data type in the JSON output. This will manually convert the numeric values using the format() function using the number of digits specified in digits, bypassing the yyjsonr handling of float values and writing the numbers out as JSON character strings. See the Dataset JSON user guide for more information. Defaults to FALSE
digits	When using float_as_decimals, the number of digits to use when writing out floats. Going higher than 16 may start writing otherwise sufficiently precise decimals (i.e. .2) to long strings.

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)

---