LTP2, PMRI, and PDAC Report Generators

This package contains only the three Python scripts for generating the LTP2, PMRI, and PDAC validation reports. Raw validation data and generated reports are not included.

Requirements

• Python 3.10 or newer
• pandas

Create a virtual environment and install the dependency:

python3 -m venv .venv
source .venv/bin/activate
python -m pip install pandas

On Windows, activate with .venv\Scripts\activate.

Run

Run commands from this folder and replace the example paths with the recipient's raw CSV and output paths.

LTP2, for one raw validation CSV:

python generate_ldyt_reports.py "/path/to/LTP2-raw-validation.csv" --output-dir "/path/to/output"

PMRI, for one raw validation CSV:

python generate_pmri_reports.py "/path/to/PMRI-raw-validation.csv"

The PMRI reports are written beside the input CSV. To choose their output folder, place the source CSV in that folder or update output_paths in generate_pmri_reports.py before running.

PDAC, for one or more site CSVs:

python build_pdac_reports.py --input-files "/path/to/BCM.csv" "/path/to/UPMC.csv" --output-dir "/path/to/output"

Run any script with --help to see its options. The scripts have defaults from the original workstation; pass input and output paths explicitly so they work on another computer. Inputs must be the corresponding raw validation exports and include the columns expected by that project's script.

Included code

• generate_ldyt_reports.py: LTP2 PHI, validation detail/summary, and pivot reports.
• generate_pmri_reports.py: PMRI PHI, validation detail/summary, and pivot reports.
• build_pdac_reports.py: PDAC per-site validation, PHI, and pivot reports.

These scripts process potentially sensitive validation data. Share the scripts separately from any raw data or generated reports, and review output files before distribution.