README.md

In UW-GAC/AnvilDataModels: Utilities for AnVIL data models

AnvilDataModels

R package to work with AnVIL data models

This R package provides utilities for:

• converting a data model from TSV to DBML format
• checking a set of data tables against a data model
• generating a markdown report summarizing data model checks
• importing data tables into AnVIL

Data model specification

Data models should be specified in one or more JSON files.

The JSON file should contain a list "tables". Each table object should contain the following elements:

• table: table name
• columns: list of "column" objects
• required: TRUE indicates the table is required, FALSE or missing if the table is optional. 'CONDITIONAL (t1)' indicates that a table is only required if table 't1' is present.

Each column object can contain the following elements. 'column' and 'data_type' are required.

• column: column name
• data_type: "string", "boolean, "integer", "float", "date", "dateTime", or "enumeration"
• enumerations: if data_type is enumeration, list values here
• multi_value_delimiter: if data values may be delimited, this contains the delimiter value
• required: TRUE indicates the column is required, FALSE or missing if the column is optional. 'CONDITIONAL (column = value)' indicates a requirement only if any element of 'column' contains 'value'. 'CONDITIONAL (column)' indicates a requirement only if any element of 'column' is non-missing.
• primary_key: logical where TRUE indicates the column is a primary key, other values may be FALSE or missing
• references: Reference to other columns in the data model. Either of
  • a cross-table reference string following the DBML format
  • 'from:' followed by a comma-separated list of columns used to automatically generate this column using a hash function.
• description: Note string (column description) following the DBML format

Examples

• Example data model file
• Example data model with an automatically-generated column
• Example data model with conditional requirements

UW-GAC/AnvilDataModels documentation built on Nov. 3, 2024, 7:33 p.m.