10  CM Listing

Objectives

This guide demonstrates Concomitant Medications (CM) listing showing detailed individual medication records.

10.1 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_cm_listing
from csrlite.cm.cm_listing import cm_listing

10.2 Concomitant Medications Listing

Shows detailed individual concomitant medications with categories, terms, and dosing information.

10.3 StudyPlan-Driven Workflow

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

2026-02-03 15:27:14,679 - csrlite.common.plan - INFO - Successfully loaded dataset 'adsl' from 'studies/xyz123/yaml/../../../data/adsl.parquet'
2026-02-03 15:27:14,682 - csrlite.common.plan - INFO - Successfully loaded dataset 'adae' from 'studies/xyz123/yaml/../../../data/adae.parquet'
2026-02-03 15:27:14,684 - csrlite.common.plan - INFO - Successfully loaded dataset 'adie' from 'studies/xyz123/yaml/../../../data/adie.parquet'
2026-02-03 15:27:14,685 - 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_cm_listing(study_plan)

10.4 Complete Pipeline

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

# Define output path
output_rtf = "studies/xyz123/rtf/cm_listing_manual.rtf"
# Ensure directory exists
Path(output_rtf).parent.mkdir(parents=True, exist_ok=True)

pd_listing_path = cm_listing(
    population=adsl,
    observation=adcm,
    population_filter="SAFFL = 'Y'",
    observation_filter="CONFL = 'Y'", # On-treatment/Concomitant
    parameter_filter=None,
    id=("USUBJID", "Subject ID"),
    title=[
        "Listing of Concomitant Medications",
        "(Safety Population)"
    ],
    footnote=["Medications are sorted by treatment and subject ID."],
    source=["Source: ADSL and ADCM datasets"],
    output_file=output_rtf,
    population_columns=[
        ("TRT01A", "Treatment"),
        ("AGE", "Age"),
        ("SEX", "Sex")
    ],
    observation_columns=[
        ("CMSEQ", "Sequence"),
        ("CMTRT", "Medication"),
        ("CMDECOD", "Standardized Name"),
        ("ASTDT", "Start Date"),
        ("AENDT", "End Date"),
        ("CMDOSE", "Dose"),
        ("CMDOSU", "Unit"),
        ("CMROUTE", "Route"),
        ("CMFREQ", "Frequency"),
        ("CMINDC", "Indication")
    ],
    sort_columns=["TRT01A", "USUBJID", "ASTDT", "CMSEQ"],
    group_by=["USUBJID"],
    page_by=["TRT01A"],
)
print(f"Generated: {pd_listing_path}")

studies/xyz123/rtf/cm_listing_manual.rtf
Generated: studies/xyz123/rtf/cm_listing_manual.rtf