cehrgpt 0.1.2__py3-none-any.whl → 0.1.4__py3-none-any.whl

cehrgpt/analysis/treatment_pathway/diabetes_treatment_pathway.py

@@ -0,0 +1,94 @@
+#!/usr/bin/env python
+"""
+Diabetes Treatment Pathways Study Script.
+
+Specialized script for analyzing diabetes treatment pathways using OMOP CDM data.
+Uses the generalized treatment_pathway module with diabetes-specific parameters.
+"""
+
+import argparse
+import sys
+
+from cehrgpt.analysis.treatment_pathway.treatment_pathway import main as treatment_main
+
+# Diabetes-specific configuration
+DIABETES_CONFIG = {
+    "study_name": "DIABETES",
+    "drug_concepts": [21600712, 21500148],
+    "target_conditions": [201820],
+    "exclusion_conditions": [444094, 35506621],
+}
+
+
+def parse_diabetes_arguments():
+    """Parse command line arguments specific to diabetes study."""
+    parser = argparse.ArgumentParser(
+        description="Analyze diabetes treatment pathways using OMOP CDM data"
+    )
+
+    parser.add_argument(
+        "--omop-folder",
+        required=True,
+        help="Path to OMOP CDM data folder containing parquet files",
+    )
+
+    parser.add_argument(
+        "--output-folder", required=True, help="Output folder for results"
+    )
+
+    parser.add_argument(
+        "--app-name",
+        default="Diabetes_Treatment_Pathways",
+        help="Spark application name (default: Diabetes_Treatment_Pathways)",
+    )
+
+    parser.add_argument(
+        "--spark-master",
+        default="local[*]",
+        help="Spark master URL (default: local[*])",
+    )
+
+    return parser.parse_args()
+
+
+def main():
+    """Main function that overwrites sys.argv and calls the generalized treatment pathway main."""
+    diabetes_args = parse_diabetes_arguments()
+
+    print("Diabetes Treatment Pathways Analysis")
+    print("=" * 50)
+    print(f"Study Configuration:")
+    print(f"  - Study Name: {DIABETES_CONFIG['study_name']}")
+    print(f"  - Drug Concepts: {DIABETES_CONFIG['drug_concepts']}")
+    print(f"  - Target Conditions: {DIABETES_CONFIG['target_conditions']}")
+    print(f"  - Exclusion Conditions: {DIABETES_CONFIG['exclusion_conditions']}")
+    print(f"  - OMOP Folder: {diabetes_args.omop_folder}")
+    print(f"  - Output Folder: {diabetes_args.output_folder}")
+    print("=" * 50)
+
+    # Overwrite sys.argv with the generalized treatment pathway arguments
+    sys.argv = [
+        "treatment_pathway.py",
+        "--omop-folder",
+        diabetes_args.omop_folder,
+        "--output-folder",
+        diabetes_args.output_folder,
+        "--drug-concepts",
+        ",".join(map(str, DIABETES_CONFIG["drug_concepts"])),
+        "--target-conditions",
+        ",".join(map(str, DIABETES_CONFIG["target_conditions"])),
+        "--exclusion-conditions",
+        ",".join(map(str, DIABETES_CONFIG["exclusion_conditions"])),
+        "--app-name",
+        diabetes_args.app_name,
+        "--spark-master",
+        diabetes_args.spark_master,
+        "--study-name",
+        DIABETES_CONFIG["study_name"],
+    ]
+    # Parse arguments using the generalized script's parser and call its main function
+    treatment_main()
+
+
+if __name__ == "__main__":
+    main()

cehrgpt/analysis/treatment_pathway/htn_treatment_pathway.py

@@ -0,0 +1,94 @@
+#!/usr/bin/env python
+"""
+HTN Treatment Pathways Study Script.
+
+Specialized script for analyzing hypertension treatment pathways using OMOP CDM data.
+Uses the generalized treatment_pathway module with HTN-specific parameters.
+"""
+
+import argparse
+import sys
+
+from cehrgpt.analysis.treatment_pathway.treatment_pathway import main as treatment_main
+
+# HTN-specific configuration
+HTN_CONFIG = {
+    "study_name": "HTN",
+    "drug_concepts": [21600381, 21601461, 21601560, 21601664, 21601744, 21601782],
+    "target_conditions": [316866],
+    "exclusion_conditions": [444094],
+}
+
+
+def parse_htn_arguments():
+    """Parse command line arguments specific to HTN study."""
+    parser = argparse.ArgumentParser(
+        description="Analyze hypertension treatment pathways using OMOP CDM data"
+    )
+
+    parser.add_argument(
+        "--omop-folder",
+        required=True,
+        help="Path to OMOP CDM data folder containing parquet files",
+    )
+
+    parser.add_argument(
+        "--output-folder", required=True, help="Output folder for results"
+    )
+
+    parser.add_argument(
+        "--app-name",
+        default="HTN_Treatment_Pathways",
+        help="Spark application name (default: HTN_Treatment_Pathways)",
+    )
+
+    parser.add_argument(
+        "--spark-master",
+        default="local[*]",
+        help="Spark master URL (default: local[*])",
+    )
+
+    return parser.parse_args()
+
+
+def main():
+    """Main function that overwrites sys.argv and calls the generalized treatment pathway main."""
+    htn_args = parse_htn_arguments()
+
+    print("HTN Treatment Pathways Analysis")
+    print("=" * 50)
+    print(f"Study Configuration:")
+    print(f"  - Study Name: {HTN_CONFIG['study_name']}")
+    print(f"  - Drug Concepts: {HTN_CONFIG['drug_concepts']}")
+    print(f"  - Target Conditions: {HTN_CONFIG['target_conditions']}")
+    print(f"  - Exclusion Conditions: {HTN_CONFIG['exclusion_conditions']}")
+    print(f"  - OMOP Folder: {htn_args.omop_folder}")
+    print(f"  - Output Folder: {htn_args.output_folder}")
+    print("=" * 50)
+
+    # Overwrite sys.argv with the generalized treatment pathway arguments
+    sys.argv = [
+        "treatment_pathway.py",
+        "--omop-folder",
+        htn_args.omop_folder,
+        "--output-folder",
+        htn_args.output_folder,
+        "--drug-concepts",
+        ",".join(map(str, HTN_CONFIG["drug_concepts"])),
+        "--target-conditions",
+        ",".join(map(str, HTN_CONFIG["target_conditions"])),
+        "--exclusion-conditions",
+        ",".join(map(str, HTN_CONFIG["exclusion_conditions"])),
+        "--app-name",
+        htn_args.app_name,
+        "--spark-master",
+        htn_args.spark_master,
+        "--study-name",
+        HTN_CONFIG["study_name"],
+    ]
+    # Parse arguments using the generalized script's parser and call its main function
+    treatment_main()
+
+
+if __name__ == "__main__":
+    main()