#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ 从 PostgreSQL 导出患者首页复核表，并把人工复核结果回写到 Patient_FrontPages。 依赖系统命令 psql；数据库密码通过 PGPASSWORD 环境变量或 --pg-password 传入。 """ from __future__ import annotations import argparse import os import re import shutil import subprocess import sys import tempfile from pathlib import Path PROJECT_ROOT = Path(__file__).resolve().parents[2] DEFAULT_OUTPUT = PROJECT_ROOT / "数据处理结果区" / "04_复核与人工校正" / "患者首页_人工复核表.csv" DEFAULT_TABLE = "Patient_FrontPages" def quote_pg_identifier(identifier: str) -> str: if not re.fullmatch(r"[A-Za-z_][A-Za-z0-9_]*", identifier): raise ValueError(f"非法 PostgreSQL 表名：{identifier}") return '"' + identifier.replace('"', '""') + '"' def connection_env(args: argparse.Namespace) -> dict[str, str]: env = os.environ.copy() env.update( { "PGHOST": args.pg_host or os.environ.get("PGHOST", ""), "PGPORT": str(args.pg_port or os.environ.get("PGPORT", "")), "PGDATABASE": args.pg_database or os.environ.get("PGDATABASE", ""), "PGUSER": args.pg_user or os.environ.get("PGUSER", ""), "PGPASSWORD": args.pg_password or os.environ.get("PGPASSWORD", ""), } ) missing = [name for name in ["PGHOST", "PGPORT", "PGDATABASE", "PGUSER", "PGPASSWORD"] if not env.get(name)] if missing: raise RuntimeError("缺少 PostgreSQL 连接配置：" + "、".join(missing)) return env def run_psql(sql: str, args: argparse.Namespace) -> None: if shutil.which("psql") is None: raise RuntimeError("未找到 psql。请先安装 PostgreSQL 客户端。") with tempfile.TemporaryDirectory(prefix="patient_front_review_") as tmpdir: sql_path = Path(tmpdir) / "review.sql" sql_path.write_text(sql, encoding="utf-8") completed = subprocess.run( ["psql", "--no-password", "--file", str(sql_path)], check=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True, encoding="utf-8", errors="replace", env=connection_env(args), ) if completed.returncode != 0: raise RuntimeError(completed.stderr.strip() or completed.stdout.strip() or "psql 执行失败") if completed.stdout.strip(): print(completed.stdout.strip()) def export_review(args: argparse.Namespace) -> None: output = args.output.resolve() output.parent.mkdir(parents=True, exist_ok=True) escaped_output = str(output).replace("'", "''") table = quote_pg_identifier(args.pg_table) where_sql = "" if args.all else "WHERE review_status <> 'auto_pass' OR manual_corrected IS TRUE" select_sql = ( "SELECT inpatient_no, source_file, medical_record_no, front_page_medical_record_no, patient_name, " "gender, birth_date, discharge_dept, major_department, primary_diagnosis, " "primary_diagnosis_code, total_cost, self_pay_amount, review_status, " "review_notes::text AS review_notes, auto_corrections::text AS auto_corrections, " "manual_corrected, contact_address, contact_phone, discharge_diagnoses::text AS discharge_diagnoses, " "operations::text AS operations, pathology_diagnosis, pathology_diagnosis_code, pathology_no, " "discharge_disposition_code, readmission_plan_code, quality_status, quality_notes::text AS quality_notes, " "'' AS manual_review_notes, '' AS corrected_medical_record_no, " "'' AS corrected_patient_name, '' AS corrected_major_department, " "'' AS corrected_primary_diagnosis, '' AS corrected_primary_diagnosis_code, " "'' AS corrected_total_cost, '' AS corrected_self_pay_amount, '' AS mark_review_status " f"FROM {table} {where_sql} ORDER BY source_file" ) sql = f"\\set ON_ERROR_STOP on\n\\copy ({select_sql}) TO '{escaped_output}' WITH (FORMAT csv, HEADER true, ENCODING 'UTF8')\n" run_psql(sql, args) print(f"已导出复核表：{output}") def import_review(args: argparse.Namespace) -> None: input_path = args.input.resolve() if not input_path.exists(): raise RuntimeError(f"复核表不存在：{input_path}") escaped_input = str(input_path).replace("'", "''") table = quote_pg_identifier(args.pg_table) sql = f""" \\set ON_ERROR_STOP on CREATE TEMP TABLE patient_front_review_import ( inpatient_no TEXT, source_file TEXT, medical_record_no TEXT, front_page_medical_record_no TEXT, patient_name TEXT, gender TEXT, birth_date TEXT, discharge_dept TEXT, major_department TEXT, primary_diagnosis TEXT, primary_diagnosis_code TEXT, total_cost TEXT, self_pay_amount TEXT, review_status TEXT, review_notes TEXT, auto_corrections TEXT, manual_corrected TEXT, contact_address TEXT, contact_phone TEXT, discharge_diagnoses TEXT, operations TEXT, pathology_diagnosis TEXT, pathology_diagnosis_code TEXT, pathology_no TEXT, discharge_disposition_code TEXT, readmission_plan_code TEXT, quality_status TEXT, quality_notes TEXT, manual_review_notes TEXT, corrected_medical_record_no TEXT, corrected_patient_name TEXT, corrected_major_department TEXT, corrected_primary_diagnosis TEXT, corrected_primary_diagnosis_code TEXT, corrected_total_cost TEXT, corrected_self_pay_amount TEXT, mark_review_status TEXT ); \\copy patient_front_review_import FROM '{escaped_input}' WITH (FORMAT csv, HEADER true, ENCODING 'UTF8') UPDATE {table} AS t SET medical_record_no = COALESCE(NULLIF(i.corrected_medical_record_no, ''), t.medical_record_no), patient_name = COALESCE(NULLIF(i.corrected_patient_name, ''), t.patient_name), major_department = COALESCE(NULLIF(i.corrected_major_department, ''), t.major_department), primary_diagnosis = COALESCE(NULLIF(i.corrected_primary_diagnosis, ''), t.primary_diagnosis), primary_diagnosis_code = COALESCE(NULLIF(i.corrected_primary_diagnosis_code, ''), t.primary_diagnosis_code), total_cost = COALESCE(NULLIF(i.corrected_total_cost, '')::numeric, t.total_cost), self_pay_amount = COALESCE(NULLIF(i.corrected_self_pay_amount, '')::numeric, t.self_pay_amount), review_status = COALESCE(NULLIF(i.mark_review_status, ''), 'reviewed'), review_notes = CASE WHEN NULLIF(i.manual_review_notes, '') IS NULL THEN t.review_notes ELSE t.review_notes || jsonb_build_array(i.manual_review_notes) END, manual_corrected = CASE WHEN NULLIF(i.corrected_medical_record_no, '') IS NOT NULL OR NULLIF(i.corrected_patient_name, '') IS NOT NULL OR NULLIF(i.corrected_major_department, '') IS NOT NULL OR NULLIF(i.corrected_primary_diagnosis, '') IS NOT NULL OR NULLIF(i.corrected_primary_diagnosis_code, '') IS NOT NULL OR NULLIF(i.corrected_total_cost, '') IS NOT NULL OR NULLIF(i.corrected_self_pay_amount, '') IS NOT NULL OR lower(COALESCE(i.manual_corrected, '')) IN ('true', 't', '1', 'yes', 'y') THEN true ELSE t.manual_corrected END FROM patient_front_review_import AS i WHERE ( NULLIF(i.inpatient_no, '') IS NOT NULL AND t.inpatient_no = i.inpatient_no ) OR ( NULLIF(i.inpatient_no, '') IS NULL AND t.source_file = i.source_file ); """.strip() run_psql(sql, args) print(f"已回写人工复核表：{input_path}") def build_parser() -> argparse.ArgumentParser: parser = argparse.ArgumentParser(description="导出/回写患者首页 PostgreSQL 人工复核表。") subparsers = parser.add_subparsers(dest="command", required=True) def add_pg_options(subparser: argparse.ArgumentParser) -> None: subparser.add_argument("--pg-host", default=os.environ.get("PGHOST", ""), help="PostgreSQL 主机；也可用 PGHOST") subparser.add_argument("--pg-port", default=os.environ.get("PGPORT", "5432"), help="PostgreSQL 端口；也可用 PGPORT") subparser.add_argument("--pg-database", default=os.environ.get("PGDATABASE", ""), help="PostgreSQL 数据库；也可用 PGDATABASE") subparser.add_argument("--pg-user", default=os.environ.get("PGUSER", ""), help="PostgreSQL 用户名；也可用 PGUSER") subparser.add_argument("--pg-password", default=os.environ.get("PGPASSWORD", ""), help="PostgreSQL 密码；也可用 PGPASSWORD") subparser.add_argument("--pg-table", default=os.environ.get("PG_PATIENT_TABLE", DEFAULT_TABLE), help="PostgreSQL 表名") export_parser = subparsers.add_parser("export", help="从 PostgreSQL 导出待复核 CSV") add_pg_options(export_parser) export_parser.add_argument("-o", "--output", type=Path, default=DEFAULT_OUTPUT, help="复核 CSV 输出路径") export_parser.add_argument("--all", action="store_true", help="导出全部记录，而不仅是需复核/已人工修正记录") import_parser = subparsers.add_parser("import", help="把人工复核 CSV 回写 PostgreSQL") add_pg_options(import_parser) import_parser.add_argument("-i", "--input", type=Path, default=DEFAULT_OUTPUT, help="人工复核 CSV 路径") return parser def main() -> int: args = build_parser().parse_args() if args.command == "export": export_review(args) elif args.command == "import": import_review(args) else: raise RuntimeError(f"未知命令：{args.command}") return 0 if __name__ == "__main__": try: raise SystemExit(main()) except Exception as exc: # noqa: BLE001 - 命令行工具需要清楚输出错误 print(f"错误：{exc}", file=sys.stderr) raise SystemExit(1)