init: 初始化 dpb 桃育种系统代码库
前后端 + 后端 FastAPI 全量源码、部署脚本与文档。
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"""波次5.1 数据治理：bre_* 表审计列统一到新契约。
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新契约（与 core/base_model.py ModelMixin + UserMixin 一致）：
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id / uuid(unique) / is_deleted(bool) / created_time / updated_time / deleted_time /
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created_id / updated_id / deleted_id
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处理三类历史表（全部幂等，可重复执行）：
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- 旧式表（is_deleted=int，遗留 created_by/updated_by 列，缺 uuid/deleted_time）：
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补 uuid（回填 gen_random_uuid + 唯一索引）、补 deleted_time、
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is_deleted int→boolean、删除 created_by/updated_by（先并入 created_id/updated_id）。
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- 缺审计列表（bre_prediction_value / bre_audit_log / bre_statistics_job）：
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补缺列（uuid/is_deleted/deleted_time/updated_time）。
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- 新式表残留死列（created_by/updated_by）：直接删除。
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说明：
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- 旧式表既有 created_id（新）又有 created_by（旧），合并时以 created_id 优先。
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- 统计 4 表（prediction/prediction_value/combining_ability/statistics_job）已接 ORM，
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补 created_deleted 索引与 ORM __table_args__ 对齐。
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"""
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import asyncio
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import os
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import sys
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BACKEND_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
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sys.path.insert(0, BACKEND_DIR)
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os.environ.setdefault("ENVIRONMENT", "dev")
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# 旧式表：is_deleted=int + created_by/updated_by 遗留，缺 uuid/deleted_time
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GROUP_A = [
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"bre_marker", "bre_genotype_call", "bre_genotype_sample", "bre_genotyping_dataset",
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"bre_environment_condition", "bre_field_operation", "bre_group_member", "bre_observation",
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"bre_planting_treatment", "bre_prediction", "bre_propagation", "bre_report", "bre_seed_lot",
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"bre_combining_ability",
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]
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# 特殊：bre_statistics_job 缺 uuid/deleted_time/updated_time，且有 created_by 遗留
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GROUP_C = ["bre_statistics_job"]
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# 缺审计列：uuid/is_deleted/deleted_time/updated_time 全缺（无 created_by 遗留）
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GROUP_B = ["bre_prediction_value", "bre_audit_log"]
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# 新式表残留 created_by/updated_by 死列
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GROUP_D = [
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"bre_group", "bre_pedigree", "bre_plan", "bre_selection_rule", "bre_trait",
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"bre_treatment", "bre_trial", "bre_trial_study", "bre_trial_study_entry",
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]
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# 统计 4 表补 created_deleted 索引（与 ORM __table_args__ 对齐）
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INDEX_TABLES = ["bre_prediction", "bre_prediction_value", "bre_combining_ability", "bre_statistics_job"]
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async def column_exists(db, table: str, col: str) -> bool:
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from sqlalchemy import text
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r = await db.execute(text(
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"SELECT 1 FROM information_schema.columns WHERE table_name=:t AND column_name=:c"
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), {"t": table, "c": col})
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return r.scalar() is not None
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async def index_exists(db, table: str, idx: str) -> bool:
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from sqlalchemy import text
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r = await db.execute(text(
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"SELECT 1 FROM pg_indexes WHERE schemaname='public' AND tablename=:t AND indexname=:i"
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), {"t": table, "i": idx})
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return r.scalar() is not None
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async def column_type(db, table: str, col: str) -> str:
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from sqlalchemy import text
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r = await db.execute(text(
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"SELECT data_type FROM information_schema.columns WHERE table_name=:t AND column_name=:c"
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), {"t": table, "c": col})
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return (r.scalar() or "").lower()
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async def ensure_uuid(db, table: str) -> None:
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from sqlalchemy import text
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if not await column_exists(db, table, "uuid"):
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await db.execute(text(f"ALTER TABLE {table} ADD COLUMN uuid VARCHAR(64)"))
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await db.execute(text(
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f"UPDATE {table} SET uuid = gen_random_uuid()::varchar WHERE uuid IS NULL OR btrim(uuid) = ''"
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))
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await db.execute(text(f"ALTER TABLE {table} ALTER COLUMN uuid SET NOT NULL"))
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idx = f"ix_{table}_uuid"
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if not await index_exists(db, table, idx):
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await db.execute(text(f"CREATE UNIQUE INDEX {idx} ON {table} (uuid)"))
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async def ensure_column(db, table: str, col: str, ddl: str) -> None:
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from sqlalchemy import text
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if not await column_exists(db, table, col):
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await db.execute(text(ddl))
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async def drop_legacy_audit(db, table: str) -> None:
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"""合并旧列数据到新列后删除 created_by/updated_by 死列。"""
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from sqlalchemy import text
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if await column_exists(db, table, "created_by"):
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await db.execute(text(
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f"UPDATE {table} SET created_id = created_by "
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f"WHERE created_id IS NULL AND created_by IS NOT NULL"
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))
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await db.execute(text(f"ALTER TABLE {table} DROP COLUMN created_by"))
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if await column_exists(db, table, "updated_by"):
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await db.execute(text(
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f"UPDATE {table} SET updated_id = updated_by "
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f"WHERE updated_id IS NULL AND updated_by IS NOT NULL"
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))
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await db.execute(text(f"ALTER TABLE {table} DROP COLUMN updated_by"))
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async def convert_is_deleted(db, table: str) -> None:
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from sqlalchemy import text
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t = await column_type(db, table, "is_deleted")
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if t != "integer":
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return
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bad = (await db.execute(text(
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f"SELECT COUNT(*) FROM {table} WHERE is_deleted IS NULL OR is_deleted NOT IN (0,1)"
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))).scalar() or 0
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if bad:
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raise RuntimeError(f"{table}.is_deleted 含非 0/1 值 {bad} 行，拒绝转换")
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# 先去掉整数默认值（0），否则类型转换会因默认值无法转换而失败
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await db.execute(text(f"ALTER TABLE {table} ALTER COLUMN is_deleted DROP DEFAULT"))
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await db.execute(text(
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f"ALTER TABLE {table} ALTER COLUMN is_deleted TYPE BOOLEAN USING (is_deleted::int::boolean)"
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))
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await db.execute(text(f"ALTER TABLE {table} ALTER COLUMN is_deleted SET DEFAULT false"))
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async def ensure_created_deleted_index(db, table: str) -> None:
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from sqlalchemy import text
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idx = f"ix_{table}_created_deleted"
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if not await index_exists(db, table, idx):
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await db.execute(text(
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f"CREATE INDEX {idx} ON {table} (created_time, is_deleted)"
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))
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async def main() -> None:
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from sqlalchemy import text
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from app.core.database import async_db_session
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done: list[str] = []
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async with async_db_session() as db:
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for t in GROUP_A:
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await ensure_uuid(db, t)
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await ensure_column(db, t, "deleted_time", f"ALTER TABLE {t} ADD COLUMN deleted_time TIMESTAMPTZ")
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await convert_is_deleted(db, t)
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await drop_legacy_audit(db, t)
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await db.commit()
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done.append(f"{t} (old-style)")
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for t in GROUP_C:
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await ensure_uuid(db, t)
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await ensure_column(db, t, "deleted_time", f"ALTER TABLE {t} ADD COLUMN deleted_time TIMESTAMPTZ")
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await convert_is_deleted(db, t)
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await drop_legacy_audit(db, t)
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if not await column_exists(db, t, "updated_time"):
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await db.execute(text(
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f"ALTER TABLE {t} ADD COLUMN updated_time TIMESTAMPTZ DEFAULT now() NOT NULL"
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))
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await db.commit()
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done.append(f"{t} (old-style, 补 updated_time)")
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for t in GROUP_B:
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await ensure_uuid(db, t)
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await ensure_column(db, t, "is_deleted", f"ALTER TABLE {t} ADD COLUMN is_deleted BOOLEAN DEFAULT false NOT NULL")
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await ensure_column(db, t, "deleted_time", f"ALTER TABLE {t} ADD COLUMN deleted_time TIMESTAMPTZ")
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if not await column_exists(db, t, "updated_time"):
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await db.execute(text(
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f"ALTER TABLE {t} ADD COLUMN updated_time TIMESTAMPTZ DEFAULT now() NOT NULL"
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))
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await db.commit()
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done.append(f"{t} (缺审计列)")
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for t in GROUP_D:
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await drop_legacy_audit(db, t)
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await db.commit()
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done.append(f"{t} (删死列)")
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for t in INDEX_TABLES:
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await ensure_created_deleted_index(db, t)
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await db.commit()
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done.append(f"{t} (created_deleted 索引)")
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print("完成 " + str(len(done)) + " 项迁移：")
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for d in done:
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print(" - " + d)
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if __name__ == "__main__":
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asyncio.run(main())
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