CORE Rule Builder

RuleBuilder is a Python package for processing CDISC conformance rules. It provides a RuleBuilder class that can be used to read rule definitions from an Excel file or a YAML file, and then process those rules by applying them to datasets. Here is a list of steps that it performs:

• Read rule definition. Here is a list of available rule definitions:
  • FDA_VR1_6: FDA Validator Rules v1.6 December 2022_0
  • SDTM_V2_0: SDTM and SDTMIG Conformance Rules_v2.0
  • SEND_V4_0: SEND Conformance Rules v4.0
  • ADAM_V4_0: ADaM Conformance Rules v4.0
• Get rule statistics if get_db_rule or pub2db is enabled.
• Back up current rule(s)
• Get existing rule if the rule exists in the database or in local rule folder
• Check rule citation against rule definition
• Add missing citations to the rule
• Write the rule to target folders in JSON and YAML formats
• Publish the rule to the database if pub2db is enabled

Installation

To install RuleBuilder class, run the following command:

pip install crbuilder

Usage

The RuleBuilder class can be used to process conformance rules with many commands and options. It can perform the following tasks:

• initialize the rule builder,
• get statistics for documents in a container
• build a single rule, or process a list of rules or all rules.

Here is the command line usage:

Usage: rulebuilder.py [OPTIONS] COMMAND [ARGS]...

This produce a list of available commands:

Options:
  --help  Show this message and exit.

Commands:
  build-rule
  get-doc-statistics
  initialize
  process

Initialize

The initialize command is used to create a new instance of the RuleBuilder class. It takes the following command-line options:

--r_standard: the name of the standard for which the rule definitions are being processed (default: 'SDTM_V2_0')
--r_dir: the directory where the rule definitions are stored (default: None)
--i_fn: the name of the file that contains the rule definitions for the specified standard (default: 'SDTM_and_SDTMIG_Conformance_Rules_v2.0.yaml')
--core_base_url: the URL for the CORE base JSON schema (default: 'https://raw.githubusercontent.com/cdisc-org/conformance-rules-editor/main/public/schema/CORE-base.json')
--creator_url: the URL for the rule editor (default: 'https://rule-editor.cdisc.org/.auth/me')

To initialize a new instance of the RuleBuilder class, run the following command:

rulebuilder initialize

You can specify any of the command-line options described above to customize the initialization of the RuleBuilder instance.

Build a Single Rule

The build_rule command is used to build a single rule. It takes the following command-line options:

--rule_id: the ID of the rule to build (default: None)

Replace <rule_id> with the ID of the rule you want to build.

Process All Rules

The process command is used to process all rules. It takes the following command-line options:

--r_standard: The name of the standard for which the rule definitions are being processed (default='SDTM_V2_0')
--r_ids: a list of rule IDs to include (default: None)
--s_version: a list of versions to include (default: [])
--s_class: a list of classes to include (default: [])
--s_domain: a list of domains to include (default: [])
--wrt2log: a flag indicating whether to write output to a log file (default: 1)
--pub2db: a flag indicating whether to publish rules to a database (default: 0)
--get_db_rule: a flag indicating whether to get rules from a database (default: 1)
--db_name: the name of the database to use (default: None)
--ct_name: the name of the container to use (default: 'core_rules_dev')

To process all rules with the RuleBuilder class, run the following command:

python rulebuilder.py process --r_ids all  --pub2db 1

You can specify any of the command-line options described above to customize the processing of the rules. Here are a few examples:

python rulebuilder.py process --r_ids "CG0001,    CG0002, cg0015" --pub2db 1
python rulebuilder.py process --s_domain "AE,DM" --pub2db 1
python rulebuilder.py process --s_version "3.4" --pub2db 1
python rulebuilder.py process --s_class "EVT"  --pub2db 1

License

This project is licensed under the MIT License - see the LICENSE.md file for details.

History

Version 0.4.0 (planned)

• Add capability of processing FDA conformance rules
• Add log level for creating log details

Version 0.3.1

• Moved from my personal repo core-rule-builder to CDISC repo crbuilder
• Added command-line options
• Added README
• Added backup as a default behavior while getting rule definition from database

Version 0.3.0

• Added logging capability to produce a log file per rule
• Added report capability for all the rules processed
• Added reading from and publishing to the database
• Added backup capability
• Added de-duplication capability

Version 0.2.0

• Added mutiple rule processing capability
• Added error handling and message processing
• Added processing status report
• Fixed some rule bugs

Version 0.1.0

• Set up process framework
• Read rules from a local rule folder
• Produced single rule and pass rule validation