CORE Utility Programs for USDM

Set-up

1. Clone or copy this repository
2. Create a virtual environment: python -m venv venv
3. Activate virtual environment
4. Install required packages: pip install -r requirements.txt

usdm2xl.py

This program uses the CORE USDM data service to convert a specified USDM JSON file into an Excel file (in the format expected for CORE validation):

python usdm2xl.py -dp path/to/usdm/json/file

The output file will have the same name as the JSON file, but with a timestamp suffix.

run_usdm_validation.py

This is an example implementation of the validate_usdm method to demonstrate how running CORE validation of a USDM JSON file can be integrated into a Python program. The JSON file name input is hard-coded in this example, but could be replaced with variable containing the file name.

python run_usdm_validation.py

publish_local_rules.py

Currently (as of 2024-12-12) no USDM rules have been published, so there are no USDM rules available via the CDISC Library. USDM rules therefore have to be run as local rules - i.e., rules stored locally in YAML format.

To download YAML rule specifications from the CORE Rules Editor:

1. Log into the CORE rules editor.
2. Filter rules to show only USDM rules with a rule id starting with DDF:
   1. Clear the filter on the Creator column
   2. Type DDF in the Rule Ids column search box
   3. Type USDM in the Standards column search box
3. Click on the Export... button (downwards pointing arrow) and select "Export rules YAML (as filtered)"
4. Wait for the rules to be exported - they're exported as a zip file called Rules.zip (or with a suffix if you've downloaded them before) in your browser's usual download folder.
5. Unzip the rule definitions into the resources/local_rules folder

Once the rule definitions have been downloaded, run this program (publish_local_rules.py) to:

• Remove any rule specifications where the status for the corresponding CORERULES JIRA ticket is not "Unit Testing", "Awaiting QC", "QC in Progress", or "Ready to Publish".
• Add a dummy CORE-id, which is required to run validation for local rules.

python publish_local_rules.py

Prerequisites

Note that the following are required to run this program:

• A CDISC JIRA account with at least read access to the CORERULES project.
• A JIRA personal access token (PAT) (see "Creating PATs in the application" instructions here) that has been saved in an environment variable called CONFLUENCE_API_KEY.

Source

Most of the content of this repository is a static copy from the cdisc-rules-engine repository (see version.py for copied version) as a temporary fix until an updated version of the cdisc-rules-engine is available via PyPI.