12  Medical History Listing

Objectives

This guide demonstrates Medical History (MH) listing.

12.1 Setup

import os
import sys
import polars as pl
from pathlib import Path

sys.path.insert(0, 'src')

from rtflite import LibreOfficeConverter
try:
    converter = LibreOfficeConverter()
except Exception:
    converter = None
    print("WARNING: LibreOffice not found. PDF conversion will be skipped.")

from csrlite import load_plan, study_plan_to_mh_listing
from csrlite.mh.mh_listing import mh_listing

12.2 Medical History Listing

Detailed listing of each subject’s medical history.

12.3 StudyPlan-Driven Workflow

study_plan = load_plan("studies/xyz123/yaml/plan_xyz123.yaml")
study_plan.get_plan_df().filter(pl.col("analysis") == "mh_listing")

2026-02-03 15:27:29,543 - csrlite.common.plan - INFO - Successfully loaded dataset 'adsl' from 'studies/xyz123/yaml/../../../data/adsl.parquet'
2026-02-03 15:27:29,547 - csrlite.common.plan - INFO - Successfully loaded dataset 'adae' from 'studies/xyz123/yaml/../../../data/adae.parquet'
2026-02-03 15:27:29,548 - csrlite.common.plan - INFO - Successfully loaded dataset 'adie' from 'studies/xyz123/yaml/../../../data/adie.parquet'
2026-02-03 15:27:29,549 - csrlite.common.plan - INFO - Successfully loaded dataset 'adpd' from 'studies/xyz123/yaml/../../../data/adpd.parquet'

shape: (0, 5)

analysis	population	observation	parameter	group
str	str	str	str	str

output_files = study_plan_to_mh_listing(study_plan)

12.4 Complete Pipeline

# Load data
data_path = Path("data") if Path("data").exists() else Path("../data")
adsl = pl.read_parquet(data_path / "adsl.parquet")
admh = pl.read_parquet(data_path / "admh.parquet")

# Define output path for listing
output_listing_rtf = "studies/xyz123/rtf/mh_listing_manual.rtf"
# Ensure directory exists
Path(output_listing_rtf).parent.mkdir(parents=True, exist_ok=True)

listing_path = mh_listing(
    population=adsl,
    observation=admh,
    population_filter="SAFFL = 'Y'",
    observation_filter="MHOCCUR = 'Y'",
    id=("USUBJID", "Subject ID"),
    title=[
        "Listing of Medical History",
        "(Safety Population)"
    ],
    footnote=["Sorted by Treatment, Subject, and Start Date."],
    source=["Source: ADSL and ADMH datasets"],
    output_file=output_listing_rtf,
    sort_columns=["TRT01A", "USUBJID", "MHSTDTC"]
)
print(f"Generated: {listing_path}")

studies/xyz123/rtf/mh_listing_manual.rtf
Generated: studies/xyz123/rtf/mh_listing_manual.rtf