-- ============================================================
-- 桃育种系统 - 一期业务表建表 SQL（breeding 全量 14 域）
-- 依据: 后端 ORM 模型 (backend/app/api/v1/module_bre/**/model.py)
--       对齐 doc/桃育种系统业务功能规划报告.md 第九节（2026-07-28 实际落地）
-- 说明:
--   1. bre_germplasm 等表由 create_all 建；本文件为可读 schema 参考。
--   2. 审计字段(id/uuid/is_deleted/created_time/updated_time/deleted_time/
--      created_id/updated_id/deleted_id)由基类 ModelMixin/UserMixin 提供。
--   3. 外键统一引用 sys_user(id) ON DELETE SET NULL（审计人）；
--      业务外键引用本文件内表，统一 ON DELETE CASCADE（级联删除）。
--   4. 状态/类别字段以 varchar 存字典存储值（英码 dict_value，如 common/strong/alive），
--      展示中文 dict_label；[字典: <type>] 标注的字段其取值来自 sys_dict，种子见
--      bre_dict.sql，导入经 DictLabelResolver 翻译、前端经 useDictStore 取 label；
--      [字典: <type> 待补] 表示模型标注为字典字段但尚无种子 SQL，取值待定。
--   5. 育种目标独立成表 bre_target（主数据）；杂交组合单选引用其一，
--      以便后期按"组合→目标→目标性状阈值→单株达标判定"统计每组合达标率。
--   6. 育种单株独立成表 bre_tree（新增实体）；tree_evaluation /
--      tree_photo / selection_result 经 tree_id 外键关联，删树级联删下游三表。
--   7. 人员独立成表 bre_personnel（方案B）；5 个业务域经
--      bre_personnel_id 外键引用（授粉人/定植人/育苗人/评价人/种子处理人）。
--   8. 无 status 字段的表，model 中已覆盖 __table_args__ 去掉 status 索引
--      （仅保留 (created_time, is_deleted) 复合索引用于数据权限过滤）。
--   9. 日期字段以 varchar(20) 存文本日期（如 '2026-07-28'），非 timestamptz。
-- ============================================================


-- ============================================================
-- 模块1: 亲本资源管理
-- ============================================================

-- 表: bre_germplasm (亲本资源)
--   设计说明: 保存育种用种质/品种档案，作为杂交组合的母本与父本来源。
--   与其它表关系:
--     * 上游: 无
--     * 下游: 被 cross_combination(female_parent_id/male_parent_id) 引用；
--             被 bre_germplasm_photo(独立文件) 经 germplasm_id 引用
--   字典来源字段: variety_type(变种类型), firmness(硬度), maturity_period(成熟期:早/中/晚),
--                flowering_period(花期) —— 均 [字典]，见 bre_dict.sql
--   逻辑关系: 删除种质 → 级联删除其照片子表；作为母/父本被组合引用时随组合级联删除
CREATE TABLE IF NOT EXISTS bre_germplasm (
    cultivar_name        varchar(100) NOT NULL,           -- 品种/种质名称
    variety_type         varchar(20),                     -- 变种类型(普通桃/油桃/蟠桃/油蟠桃/黄肉) [字典: variety_type]
    origin               varchar(200),                   -- 来源
    preservation_site    varchar(200),                    -- 保存地
    avg_fruit_weight     numeric(8,2),                    -- 平均果重(g)
    ssc                  numeric(4,1),                     -- 可溶性固形物(%)
    firmness             varchar(20),                     -- 硬度 [字典: firmness]
    maturity_period      varchar(20),                     -- 成熟期(早/中/晚) [字典: maturity_period]
    flowering_period     varchar(20),                     -- 花期 [字典: flowering_period]
    chilling_requirement integer,                         -- 需冷量(h)
    disease_resistance   text,                            -- 抗病性描述
    can_be_female        boolean NOT NULL DEFAULT false,  -- 可作母本
    can_be_male          boolean NOT NULL DEFAULT false,  -- 可作父本
    pedigree_note        text,                            -- 系谱备注
    photo_path           varchar(500),                    -- 照片地址(图片URL)

    id              serial PRIMARY KEY,
    uuid            varchar(64) NOT NULL UNIQUE,
    is_deleted      boolean NOT NULL DEFAULT false,
    created_time    timestamptz NOT NULL DEFAULT now(),
    updated_time    timestamptz NOT NULL DEFAULT now(),
    deleted_time    timestamptz,
    created_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    updated_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    deleted_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,

    CONSTRAINT uq_bre_germplasm_uuid UNIQUE (uuid)
);
COMMENT ON TABLE bre_germplasm IS '亲本资源表(桃育种)';
CREATE INDEX IF NOT EXISTS ix_bre_germplasm_created_deleted ON bre_germplasm (created_time, is_deleted);


-- ============================================================
-- 模块2: 基地/试验地管理
-- ============================================================

-- 表: bre_site (基地/试验地)
--   设计说明: 试验基地/试验站主数据，定植与授粉的地点来源。
--   与其它表关系:
--     * 上游: 无
--     * 下游: 被 bre_plot(site_id) 引用
--   字典来源字段: eco_type(生态区类型:华北/西北/华东/西南/东北/华南) [字典]，见 bre_dict.sql
--   逻辑关系: 删除基地 → 级联删除其下所有地块
CREATE TABLE IF NOT EXISTS bre_site (
    site_name       varchar(100) NOT NULL,               -- 基地/试验地名称
    address         varchar(255),                        -- 详细地址
    area            float,                               -- 基地面积(亩)
    longitude       float,                               -- 经度
    latitude        float,                               -- 纬度
    eco_type        varchar(50),                        -- 生态区类型(华北/西北/华东/...) [字典: eco_type]
    remark          text,                                -- 备注

    id              serial PRIMARY KEY,
    uuid            varchar(64) NOT NULL UNIQUE,
    is_deleted      boolean NOT NULL DEFAULT false,
    created_time    timestamptz NOT NULL DEFAULT now(),
    updated_time    timestamptz NOT NULL DEFAULT now(),
    deleted_time    timestamptz,
    created_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    updated_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    deleted_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,

    CONSTRAINT uq_bre_site_uuid UNIQUE (uuid)
);
COMMENT ON TABLE bre_site IS '基地/试验地管理表(桃育种)';
CREATE INDEX IF NOT EXISTS ix_bre_site_created_deleted ON bre_site (created_time, is_deleted);

-- 表: bre_plot (区块: 基地内区块划分)
--   设计说明: 基地内区块划分，作为单株定植的网格位置。
--   与其它表关系:
--     * 上游: 引用 bre_site(site_id)
--     * 下游: 被 pollination(plot_id)/planting(plot_id)/tree(plot_id) 引用
--   字典来源字段: row_orientation(行向:南北行/东西行) [字典]，见 bre_dict.sql
--   逻辑关系: 删除地块 → 级联删除引用该地块的授粉/定植/单株记录
CREATE TABLE IF NOT EXISTS bre_plot (
    site_id         integer NOT NULL REFERENCES bre_site(id) ON DELETE CASCADE,  -- 所属基地
    plot_code       varchar(50) NOT NULL,               -- 区块编号/名称
    row_orientation varchar(20),                        -- 行向(南北行/东西行) [字典: row_orientation]
    row_count       integer,                            -- 行数
    col_count       integer,                            -- 每行株数
    grid_note       text,                               -- 株行距/网格说明
    area            float,                              -- 地块面积(亩)

    id              serial PRIMARY KEY,
    uuid            varchar(64) NOT NULL UNIQUE,
    is_deleted      boolean NOT NULL DEFAULT false,
    created_time    timestamptz NOT NULL DEFAULT now(),
    updated_time    timestamptz NOT NULL DEFAULT now(),
    deleted_time    timestamptz,
    created_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    updated_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    deleted_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,

    CONSTRAINT uq_bre_plot_uuid UNIQUE (uuid)
);
COMMENT ON TABLE bre_plot IS '基地内区块划分表(桃育种)';
CREATE INDEX IF NOT EXISTS ix_bre_plot_site ON bre_plot (site_id);
CREATE INDEX IF NOT EXISTS ix_bre_plot_created_deleted ON bre_plot (created_time, is_deleted);


-- ============================================================
-- 模块3: 人员花名册
-- ============================================================

-- 表: bre_personnel (人员花名册，独立人员表/方案B)
--   设计说明: 记录参与育种的人员；被 5 个业务域经 bre_personnel_id 引用，
--             作为"干活的人"（授粉人/定植人/育苗人/评价人/种子处理人）。
--   与其它表关系:
--     * 上游: 无
--     * 下游: 被 pollination/planting/seedling/tree_evaluation/seed_treatment
--             的 bre_personnel_id 引用
--   字典来源字段: gender(性别:男/女) [字典], role(角色:育种专家/技术员/管理员) [字典]，见 bre_dict.sql
--   逻辑关系: 删除人员 → 级联删除各业务记录中该人员引用（外键均 CASCADE）
CREATE TABLE IF NOT EXISTS bre_personnel (
    name            varchar(100) NOT NULL,               -- 姓名
    gender          varchar(50),                        -- 性别(男/女) [字典: gender]
    role            varchar(50),                        -- 角色(育种专家/技术员/管理员) [字典: personnel_role]
    phone           varchar(100),                       -- 联系电话
    organization    varchar(100),                       -- 所属单位
    join_date       varchar(20),                        -- 入职日期
    remark          text,                               -- 备注

    id              serial PRIMARY KEY,
    uuid            varchar(64) NOT NULL UNIQUE,
    is_deleted      boolean NOT NULL DEFAULT false,
    created_time    timestamptz NOT NULL DEFAULT now(),
    updated_time    timestamptz NOT NULL DEFAULT now(),
    deleted_time    timestamptz,
    created_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    updated_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    deleted_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,

    CONSTRAINT uq_bre_personnel_uuid UNIQUE (uuid)
);
COMMENT ON TABLE bre_personnel IS '人员花名册表(桃育种)';
CREATE INDEX IF NOT EXISTS ix_bre_personnel_created_deleted ON bre_personnel (created_time, is_deleted);


-- ============================================================
-- 模块4: 育种目标（主数据）
-- ============================================================

-- 表: bre_target (育种目标主数据)
--   设计说明: 预置"6大品种系列"(大果型/早熟/黄肉/油桃/蟠桃/加工型)等目标，由育种家维护；
--            杂交组合单选引用其一，作为该组合达标率统计的统一基准。
--   与其它表关系:
--     * 上游: 无
--     * 下游: 被 cross_combination(bre_target_id) 引用
--   字典来源字段: series(系列/品系) [字典], is_preset(是否预设:1/0) [字典]，见 bre_dict.sql
--   逻辑关系: 删除目标 → 级联删除引用它的杂交组合
CREATE TABLE IF NOT EXISTS bre_target (
    target_name     varchar(100) NOT NULL,               -- 目标名称，如"优质大果型"
    series          varchar(100),                        -- 系列/品系 [字典: series]
    description     text,                                -- 目标说明/关键性状描述
    is_preset       varchar(50),                         -- 是否预设(1/0) [字典: is_preset]
    remark          text,                                -- 备注

    id              serial PRIMARY KEY,
    uuid            varchar(64) NOT NULL UNIQUE,
    is_deleted      boolean NOT NULL DEFAULT false,
    created_time    timestamptz NOT NULL DEFAULT now(),
    updated_time    timestamptz NOT NULL DEFAULT now(),
    deleted_time    timestamptz,
    created_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    updated_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    deleted_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,

    CONSTRAINT uq_bre_target_uuid UNIQUE (uuid)
);
COMMENT ON TABLE bre_target IS '育种目标主数据表(桃育种)';
CREATE INDEX IF NOT EXISTS ix_bre_target_created_deleted ON bre_target (created_time, is_deleted);


-- ============================================================
-- 模块5: 组合选配
-- ============================================================

-- 表: bre_cross_combination (杂交组合) —— 全模块关系枢纽
--   设计说明: 记录母本/父本/育种目标/杂交方式；下游授粉/种子/育苗/定植/单株
--             均挂靠本表 combination_id，是整条育种管线的核心枢纽。
--   与其它表关系:
--     * 上游: 引用 bre_target(bre_target_id)、bre_germplasm(female_parent_id/male_parent_id)
--     * 下游: 被 pollination/seed_treatment/seedling/planting/tree/tree_evaluation/
--             tree_photo/selection_result 的 combination_id 引用（共 8 张表）
--   字典来源字段: cross_method(杂交方式:人工杂交/自然授粉/回交) [字典]，见 bre_dict.sql
--   逻辑关系: 删除组合 → 级联删除其下全部 8 张下游业务表记录
CREATE TABLE IF NOT EXISTS bre_cross_combination (
    combination_code varchar(100) NOT NULL,              -- 组合编号 YY+3位序号(自动生成)
    cross_year       integer,                            -- 杂交年份
    bre_target_id integer NOT NULL REFERENCES bre_target(id) ON DELETE CASCADE,     -- 育种目标(单选,主数据)
    female_parent_id integer REFERENCES bre_germplasm(id) ON DELETE CASCADE,             -- 母本
    male_parent_id   integer REFERENCES bre_germplasm(id) ON DELETE CASCADE,             -- 父本
    cross_method     varchar(50),                        -- 杂交方式(人工杂交/自然授粉/回交) [字典: cross_method]
    cross_date       varchar(20),                        -- 杂交日期
    seed_count       integer,                            -- 获种数
    remark           text,                               -- 备注

    id              serial PRIMARY KEY,
    uuid            varchar(64) NOT NULL UNIQUE,
    is_deleted      boolean NOT NULL DEFAULT false,
    created_time    timestamptz NOT NULL DEFAULT now(),
    updated_time    timestamptz NOT NULL DEFAULT now(),
    deleted_time    timestamptz,
    created_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    updated_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    deleted_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,

    CONSTRAINT uq_bre_cross_combination_uuid UNIQUE (uuid)
);
COMMENT ON TABLE bre_cross_combination IS '杂交组合选配表(桃育种)';
CREATE INDEX IF NOT EXISTS ix_bre_cross_combination_target ON bre_cross_combination (bre_target_id);
CREATE INDEX IF NOT EXISTS ix_bre_cross_combination_female ON bre_cross_combination (female_parent_id);
CREATE INDEX IF NOT EXISTS ix_bre_cross_combination_male ON bre_cross_combination (male_parent_id);
CREATE INDEX IF NOT EXISTS ix_bre_cross_combination_created_deleted ON bre_cross_combination (created_time, is_deleted);


-- ============================================================
-- 模块6: 杂交授粉
-- ============================================================

-- 表: bre_pollination (授粉记录)
--   设计说明: 杂交授粉过程记录，挂靠杂交组合与试验地块。
--   与其它表关系:
--     * 上游: 引用 cross_combination(combination_id)、plot(plot_id)、personnel(bre_personnel_id 授粉人)
--     * 下游: 无
--   字典来源字段: 无（本表未设字典字段）
--   逻辑关系: 删除组合/地块/授粉人 → 级联删除本记录（外键均 CASCADE）
CREATE TABLE IF NOT EXISTS bre_pollination (
    combination_id  integer NOT NULL REFERENCES bre_cross_combination(id) ON DELETE CASCADE,  -- 所属组合
    plot_id         integer REFERENCES bre_plot(id) ON DELETE CASCADE,                        -- 试验地块
    pollination_date varchar(20),                       -- 授粉日期
    flower_count    integer,                            -- 花朵数
    effective_count integer,                            -- 有效坐果数
    bre_personnel_id integer REFERENCES bre_personnel(id) ON DELETE CASCADE,             -- 授粉人
    remark          text,                               -- 备注

    id              serial PRIMARY KEY,
    uuid            varchar(64) NOT NULL UNIQUE,
    is_deleted      boolean NOT NULL DEFAULT false,
    created_time    timestamptz NOT NULL DEFAULT now(),
    updated_time    timestamptz NOT NULL DEFAULT now(),
    deleted_time    timestamptz,
    created_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    updated_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    deleted_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,

    CONSTRAINT uq_bre_pollination_uuid UNIQUE (uuid)
);
COMMENT ON TABLE bre_pollination IS '杂交授粉记录表(桃育种)';
CREATE INDEX IF NOT EXISTS ix_bre_pollination_combination ON bre_pollination (combination_id);
CREATE INDEX IF NOT EXISTS ix_bre_pollination_plot ON bre_pollination (plot_id);
CREATE INDEX IF NOT EXISTS ix_bre_pollination_personnel ON bre_pollination (bre_personnel_id);
CREATE INDEX IF NOT EXISTS ix_bre_pollination_created_deleted ON bre_pollination (created_time, is_deleted);


-- ============================================================
-- 模块7: 种子处理
-- ============================================================

-- 表: bre_seed_treatment (种子处理)
--   设计说明: 采果后种子处理（沙藏/胚培等）记录。
--   与其它表关系:
--     * 上游: 引用 cross_combination(combination_id)、personnel(bre_personnel_id 种子处理人)
--     * 下游: 无
--   字典来源字段: treatment_method(处理方式:沙藏/层积/低温冷藏/常温) [字典]，见 bre_dict.sql
--   逻辑关系: 删除组合/处理人 → 级联删除本记录（外键均 CASCADE）
CREATE TABLE IF NOT EXISTS bre_seed_treatment (
    combination_id  integer NOT NULL REFERENCES bre_cross_combination(id) ON DELETE CASCADE,  -- 所属组合
    treatment_method varchar(30),                       -- 处理方式(沙藏/层积/低温冷藏/常温) [字典: seed_treatment_method]
    treatment_start varchar(20),                        -- 处理开始日期
    treatment_end   varchar(20),                        -- 处理结束日期
    germination_rate float,                             -- 发芽率(%)
    bre_personnel_id integer REFERENCES bre_personnel(id) ON DELETE CASCADE,             -- 种子处理人
    remark          text,                               -- 备注

    id              serial PRIMARY KEY,
    uuid            varchar(64) NOT NULL UNIQUE,
    is_deleted      boolean NOT NULL DEFAULT false,
    created_time    timestamptz NOT NULL DEFAULT now(),
    updated_time    timestamptz NOT NULL DEFAULT now(),
    deleted_time    timestamptz,
    created_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    updated_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    deleted_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,

    CONSTRAINT uq_bre_seed_treatment_uuid UNIQUE (uuid)
);
COMMENT ON TABLE bre_seed_treatment IS '种子处理记录表(桃育种)';
CREATE INDEX IF NOT EXISTS ix_bre_seed_treatment_combination ON bre_seed_treatment (combination_id);
CREATE INDEX IF NOT EXISTS ix_bre_seed_treatment_personnel ON bre_seed_treatment (bre_personnel_id);
CREATE INDEX IF NOT EXISTS ix_bre_seed_treatment_created_deleted ON bre_seed_treatment (created_time, is_deleted);


-- ============================================================
-- 模块8: 杂种苗培育
-- ============================================================

-- 表: bre_seedling (杂种苗)
--   设计说明: 播种育苗记录，溯源到杂交组合；可被定植批次引用。
--   与其它表关系:
--     * 上游: 引用 cross_combination(combination_id)、personnel(bre_personnel_id 育苗人)
--     * 下游: 被 planting(seedling_id) 引用
--   字典来源字段: 无
--   逻辑关系: 删除组合/育苗人 → 级联删除本记录；删除育苗 → 级联删除引用它的定植记录
CREATE TABLE IF NOT EXISTS bre_seedling (
    combination_id  integer NOT NULL REFERENCES bre_cross_combination(id) ON DELETE CASCADE,  -- 所属组合
    sowing_date     varchar(20),                        -- 播移日期
    tray_no         varchar(100),                       -- 穴盘号
    nursery         varchar(100),                       -- 苗圃
    seedling_count  integer,                            -- 出苗数
    bre_personnel_id integer REFERENCES bre_personnel(id) ON DELETE CASCADE,             -- 育苗人
    remark          text,                               -- 备注

    id              serial PRIMARY KEY,
    uuid            varchar(64) NOT NULL UNIQUE,
    is_deleted      boolean NOT NULL DEFAULT false,
    created_time    timestamptz NOT NULL DEFAULT now(),
    updated_time    timestamptz NOT NULL DEFAULT now(),
    deleted_time    timestamptz,
    created_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    updated_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    deleted_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,

    CONSTRAINT uq_bre_seedling_uuid UNIQUE (uuid)
);
COMMENT ON TABLE bre_seedling IS '杂种苗培育记录表(桃育种)';
CREATE INDEX IF NOT EXISTS ix_bre_seedling_combination ON bre_seedling (combination_id);
CREATE INDEX IF NOT EXISTS ix_bre_seedling_personnel ON bre_seedling (bre_personnel_id);
CREATE INDEX IF NOT EXISTS ix_bre_seedling_created_deleted ON bre_seedling (created_time, is_deleted);


-- ============================================================
-- 模块9: 田间定植
-- ============================================================

-- 表: bre_planting (田间定植)
--   设计说明: 田间定植记录，关联组合/地块/育苗批次/定植人；
--             与 bre_tree 无硬外键（1 定植 → N 株，靠 combination_id+plot_id 关联，有意设计）。
--   与其它表关系:
--     * 上游: 引用 cross_combination(combination_id)、plot(plot_id)、
--             personnel(bre_personnel_id 定植人)、seedling(seedling_id 育苗批次)
--     * 下游: 无
--   字典来源字段: 无
--   逻辑关系: 删除任一上游 → 级联删除本记录；定植批次可经 seedling_id 溯源到育苗批次
CREATE TABLE IF NOT EXISTS bre_planting (
    combination_id  integer NOT NULL REFERENCES bre_cross_combination(id) ON DELETE CASCADE,  -- 所属组合
    plot_id         integer REFERENCES bre_plot(id) ON DELETE CASCADE,                        -- 试验地块
    planting_date   varchar(20),                        -- 定植日期
    tree_count      integer,                            -- 定植株数
    row_no          integer,                            -- 行号
    col_no          integer,                            -- 列号
    bre_personnel_id integer REFERENCES bre_personnel(id) ON DELETE CASCADE,             -- 定植人
    seedling_id     integer REFERENCES bre_seedling(id) ON DELETE CASCADE,                   -- 育苗批次
    remark          text,                               -- 备注

    id              serial PRIMARY KEY,
    uuid            varchar(64) NOT NULL UNIQUE,
    is_deleted      boolean NOT NULL DEFAULT false,
    created_time    timestamptz NOT NULL DEFAULT now(),
    updated_time    timestamptz NOT NULL DEFAULT now(),
    deleted_time    timestamptz,
    created_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    updated_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    deleted_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,

    CONSTRAINT uq_bre_planting_uuid UNIQUE (uuid)
);
COMMENT ON TABLE bre_planting IS '田间定植记录表(桃育种)';
CREATE INDEX IF NOT EXISTS ix_bre_planting_combination ON bre_planting (combination_id);
CREATE INDEX IF NOT EXISTS ix_bre_planting_plot ON bre_planting (plot_id);
CREATE INDEX IF NOT EXISTS ix_bre_planting_personnel ON bre_planting (bre_personnel_id);
CREATE INDEX IF NOT EXISTS ix_bre_planting_seedling ON bre_planting (seedling_id);
CREATE INDEX IF NOT EXISTS ix_bre_planting_created_deleted ON bre_planting (created_time, is_deleted);


-- ============================================================
-- 模块10: 育种单株（新增实体）
-- ============================================================

-- 表: bre_tree (育种单株)
--   设计说明: 独立单株实体（新增），单株编号全局唯一；下游评价/照片/选育均经
--             tree_id 关联本表。修复原"tree_no 自由文本无统一实体"的断点。
--   与其它表关系:
--     * 上游: 引用 cross_combination(combination_id)、plot(plot_id)
--     * 下游: 被 tree_evaluation(tree_id)/tree_photo(tree_id)/selection_result(tree_id) 引用
--   字典来源字段: status(状态:存活/淘汰/入选) [字典]，见 bre_dict.sql
--   逻辑关系: 删除单株 → 级联删除下游三表（评价/照片/选育）
CREATE TABLE IF NOT EXISTS bre_tree (
    combination_id  integer NOT NULL REFERENCES bre_cross_combination(id) ON DELETE CASCADE,  -- 所属组合
    plot_id         integer REFERENCES bre_plot(id) ON DELETE CASCADE,                        -- 试验地块
    tree_no         varchar(100) NOT NULL,               -- 单株编号(全局唯一)
    row_no          integer,                            -- 行号
    col_no          integer,                            -- 列号
    planted_date    varchar(20),                        -- 定植日期
    status          varchar(50),                        -- 状态(存活/淘汰/入选) [字典: tree_status]
    remark          text,                               -- 备注

    id              serial PRIMARY KEY,
    uuid            varchar(64) NOT NULL UNIQUE,
    is_deleted      boolean NOT NULL DEFAULT false,
    created_time    timestamptz NOT NULL DEFAULT now(),
    updated_time    timestamptz NOT NULL DEFAULT now(),
    deleted_time    timestamptz,
    created_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    updated_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    deleted_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,

    CONSTRAINT uq_bre_tree_uuid UNIQUE (uuid)
);
COMMENT ON TABLE bre_tree IS '育种单株表(桃育种)';
CREATE INDEX IF NOT EXISTS ix_bre_tree_combination ON bre_tree (combination_id);
CREATE INDEX IF NOT EXISTS ix_bre_tree_plot ON bre_tree (plot_id);
CREATE INDEX IF NOT EXISTS ix_bre_tree_created_deleted ON bre_tree (created_time, is_deleted);


-- ============================================================
-- 模块11: 单株评价（果实性状内联，无独立 fruit_trait 表）
-- ============================================================

-- 表: bre_tree_evaluation (单株评价)
--   设计说明: 单株年度评价主表；果实性状（果形/单果重/含糖量等）内联本表，
--             不单独建 breeding_fruit_trait 子表（与原规划不同）。
--   与其它表关系:
--     * 上游: 引用 cross_combination(combination_id)、tree(tree_id)、personnel(bre_personnel_id 评价人)
--     * 下游: 无
--   字典来源字段: growth_vigor(生长势:强/中/弱) [字典: growth_vigor],
--                fruit_shape(果形:圆/扁圆/椭圆) [字典: fruit_shape]，见 bre_dict.sql
--                （fruit_weight/sugar_content 为数值字段，非字典）
--   逻辑关系: 删除组合/单株/评价人 → 级联删除本记录（外键均 CASCADE）
CREATE TABLE IF NOT EXISTS bre_tree_evaluation (
    combination_id  integer NOT NULL REFERENCES bre_cross_combination(id) ON DELETE CASCADE,  -- 所属组合
    tree_id         integer NOT NULL REFERENCES bre_tree(id) ON DELETE CASCADE,               -- 关联单株
    evaluate_year   integer,                            -- 评价年份(多年)
    evaluate_date   varchar(20),                        -- 评价日期
    growth_vigor    varchar(50),                        -- 生长势(强/中/弱) [字典: growth_vigor]
    fruit_shape     varchar(50),                        -- 果形(圆/扁圆/椭圆) [字典]
    fruit_weight    float,                              -- 单果重(g)
    sugar_content   float,                              -- 含糖量(%)
    bre_personnel_id integer REFERENCES bre_personnel(id) ON DELETE CASCADE,             -- 评价人
    remark          text,                               -- 备注

    id              serial PRIMARY KEY,
    uuid            varchar(64) NOT NULL UNIQUE,
    is_deleted      boolean NOT NULL DEFAULT false,
    created_time    timestamptz NOT NULL DEFAULT now(),
    updated_time    timestamptz NOT NULL DEFAULT now(),
    deleted_time    timestamptz,
    created_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    updated_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    deleted_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,

    CONSTRAINT uq_bre_tree_evaluation_uuid UNIQUE (uuid)
);
COMMENT ON TABLE bre_tree_evaluation IS '单株评价表(桃育种)';
CREATE INDEX IF NOT EXISTS ix_bre_tree_evaluation_combination ON bre_tree_evaluation (combination_id);
CREATE INDEX IF NOT EXISTS ix_bre_tree_evaluation_tree ON bre_tree_evaluation (tree_id);
CREATE INDEX IF NOT EXISTS ix_bre_tree_evaluation_personnel ON bre_tree_evaluation (bre_personnel_id);
CREATE INDEX IF NOT EXISTS ix_bre_tree_evaluation_created_deleted ON bre_tree_evaluation (created_time, is_deleted);


-- ============================================================
-- 模块12: 单株照片
-- ============================================================

-- 表: bre_tree_photo (单株照片)
--   设计说明: 单株照片记录，关联组合与单株。
--   与其它表关系:
--     * 上游: 引用 cross_combination(combination_id)、tree(tree_id)
--     * 下游: 无
--   字典来源字段: photo_type(照片类型:全株/果实/枝干) [字典]，见 bre_dict.sql
--   逻辑关系: 删除组合/单株 → 级联删除本记录（外键均 CASCADE）
CREATE TABLE IF NOT EXISTS bre_tree_photo (
    combination_id  integer NOT NULL REFERENCES bre_cross_combination(id) ON DELETE CASCADE,  -- 所属组合
    tree_id         integer REFERENCES bre_tree(id) ON DELETE CASCADE,                        -- 关联单株
    photo_type      varchar(50),                        -- 照片类型(全株/果实/枝干) [字典: photo_type]
    photo_url       varchar(100),                       -- 照片路径/URL
    capture_date    varchar(20),                        -- 拍摄日期
    remark          text,                               -- 备注

    id              serial PRIMARY KEY,
    uuid            varchar(64) NOT NULL UNIQUE,
    is_deleted      boolean NOT NULL DEFAULT false,
    created_time    timestamptz NOT NULL DEFAULT now(),
    updated_time    timestamptz NOT NULL DEFAULT now(),
    deleted_time    timestamptz,
    created_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    updated_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    deleted_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,

    CONSTRAINT uq_bre_tree_photo_uuid UNIQUE (uuid)
);
COMMENT ON TABLE bre_tree_photo IS '单株照片表(桃育种)';
CREATE INDEX IF NOT EXISTS ix_bre_tree_photo_combination ON bre_tree_photo (combination_id);
CREATE INDEX IF NOT EXISTS ix_bre_tree_photo_tree ON bre_tree_photo (tree_id);
CREATE INDEX IF NOT EXISTS ix_bre_tree_photo_created_deleted ON bre_tree_photo (created_time, is_deleted);


-- ============================================================
-- 模块13: 选育结果（评价筛选）
-- ============================================================

-- 表: bre_selection_result (选育结果)
--   设计说明: 单株选育结论（入选/淘汰/待定），关联组合与单株。
--   与其它表关系:
--     * 上游: 引用 cross_combination(combination_id)、tree(tree_id)
--     * 下游: 无
--   字典来源字段: is_selected(选育结论:入选/淘汰/待定) [字典]，见 bre_dict.sql
--   逻辑关系: 删除组合/单株 → 级联删除本记录（外键均 CASCADE）
CREATE TABLE IF NOT EXISTS bre_selection_result (
    combination_id  integer NOT NULL REFERENCES bre_cross_combination(id) ON DELETE CASCADE,  -- 所属组合
    tree_id         integer NOT NULL REFERENCES bre_tree(id) ON DELETE CASCADE,               -- 关联单株
    selection_year  integer,                            -- 入选年份
    is_selected     varchar(50),                        -- 选育结论(入选/淘汰/待定) [字典: selection_result]
    reason          text,                               -- 入选理由
    remark          text,                               -- 备注

    id              serial PRIMARY KEY,
    uuid            varchar(64) NOT NULL UNIQUE,
    is_deleted      boolean NOT NULL DEFAULT false,
    created_time    timestamptz NOT NULL DEFAULT now(),
    updated_time    timestamptz NOT NULL DEFAULT now(),
    deleted_time    timestamptz,
    created_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    updated_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,
    deleted_id      integer REFERENCES sys_user(id) ON DELETE SET NULL,

    CONSTRAINT uq_bre_selection_result_uuid UNIQUE (uuid)
);
COMMENT ON TABLE bre_selection_result IS '选育结果表(桃育种)';
CREATE INDEX IF NOT EXISTS ix_bre_selection_result_combination ON bre_selection_result (combination_id);
CREATE INDEX IF NOT EXISTS ix_bre_selection_result_tree ON bre_selection_result (tree_id);
CREATE INDEX IF NOT EXISTS ix_bre_selection_result_created_deleted ON bre_selection_result (created_time, is_deleted);

-- ============================================================================
-- 规划新增模块（依据 桃育种系统模块扩展需求规格 v1.9 §3，2026-07-29 刷新）
-- 说明：以下表尚未实装 model，待生成器落地后由 create_all / 迁移脚本建表。
--       风格与上方 14 域一致：snake_case 表名 + 审计字段 + 外键 + (created_time, is_deleted) 索引。
-- ============================================================================

-- §3.1 性状字典（核心性状 is_core=true 固定列，扩展性状 EAV）
CREATE TABLE IF NOT EXISTS bre_trait (
    id serial NOT NULL,
    trait_code varchar(64) NOT NULL,
    trait_name varchar(128) NOT NULL,
    category varchar(32),
    data_type varchar(16) NOT NULL DEFAULT 'numeric',
    unit varchar(16),
    is_core varchar(1) NOT NULL DEFAULT '1',
    scale_json text,
    valid_min numeric(12,3),
    valid_max numeric(12,3),
    ontology_uri varchar(255),
    remark varchar(512),
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_trait PRIMARY KEY (id),
    CONSTRAINT uq_bre_trait_code UNIQUE (trait_code)
);
COMMENT ON TABLE bre_trait IS '性状字典（§3.1）；核心性状固定列承载表型，is_core=false 走 observation EAV';
CREATE INDEX IF NOT EXISTS ix_bre_trait_created_deleted ON bre_trait (created_time, is_deleted);

-- §3.2 扩展观测（EAV，物候时序 + 非核心性状）
CREATE TABLE IF NOT EXISTS bre_observation (
    id bigserial NOT NULL,
    tree_id int,
    plot_id int,
    trait_id int,
    obs_date date,
    obs_year int,
    obs_value text,
    obs_type varchar(32),
    trial_study_id int,
    operator_id int,
    remark varchar(512),
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    status int NOT NULL DEFAULT 1,
    CONSTRAINT pk_bre_observation PRIMARY KEY (id),
    CONSTRAINT fk_observation_tree FOREIGN KEY (tree_id) REFERENCES bre_tree (id),
    CONSTRAINT fk_observation_trait FOREIGN KEY (trait_id) REFERENCES bre_trait (id)
);
COMMENT ON TABLE bre_observation IS '扩展观测 EAV（§3.2）；与 tree_evaluation 经统一性状值视图归一';
CREATE INDEX IF NOT EXISTS ix_bre_observation_created_deleted ON bre_observation (created_time, is_deleted);

-- §3.3 农事操作
CREATE TABLE IF NOT EXISTS bre_field_operation (
    id bigserial NOT NULL,
    tree_id int,
    plot_id int,
    op_type varchar(32) NOT NULL,
    op_date date,
    op_detail text,
    operator_id int,
    remark varchar(512),
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    status int NOT NULL DEFAULT 1,
    CONSTRAINT pk_bre_field_operation PRIMARY KEY (id),
    CONSTRAINT fk_field_op_tree FOREIGN KEY (tree_id) REFERENCES bre_tree (id)
);
COMMENT ON TABLE bre_field_operation IS '农事操作（§3.3）';
CREATE INDEX IF NOT EXISTS ix_bre_field_operation_created_deleted ON bre_field_operation (created_time, is_deleted);

-- §3.4 MET 试验结构：试验 / 研究 / 参试项
CREATE TABLE IF NOT EXISTS bre_trial (
    id serial NOT NULL,
    trial_name varchar(128) NOT NULL,
    trial_type varchar(32),
    design_type varchar(32),
    start_year int,
    end_year int,
    objective varchar(512),
    remark varchar(512),
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_trial PRIMARY KEY (id)
);
CREATE TABLE IF NOT EXISTS bre_trial_study (
    id serial NOT NULL,
    trial_id int,
    study_name varchar(128) NOT NULL,
    site_id int,
    year int,
    block_count int,
    design_type varchar(32),
    remark varchar(512),
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_trial_study PRIMARY KEY (id),
    CONSTRAINT fk_trial_study_trial FOREIGN KEY (trial_id) REFERENCES bre_trial (id),
    CONSTRAINT fk_trial_study_site FOREIGN KEY (site_id) REFERENCES bre_site (id)
);
CREATE TABLE IF NOT EXISTS bre_trial_study_entry (
    id serial NOT NULL,
    trial_study_id int,
    entry_number int,
    germplasm_id int,
    combination_id int,
    remark varchar(512),
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_study_entry PRIMARY KEY (id),
    CONSTRAINT fk_study_entry_study FOREIGN KEY (trial_study_id) REFERENCES bre_trial_study (id),
    CONSTRAINT fk_study_entry_germplasm FOREIGN KEY (germplasm_id) REFERENCES bre_germplasm (id)
);
COMMENT ON TABLE bre_trial IS 'MET 试验（§3.4）';
COMMENT ON TABLE bre_trial_study IS 'MET 研究（多年点，block 随机效应来源）';
COMMENT ON TABLE bre_trial_study_entry IS '参试项（design matrix 聚合键 entry_number）';

-- §3.5 分组/标签（family 虚拟 + category 复用）
CREATE TABLE IF NOT EXISTS bre_group (
    id serial NOT NULL,
    group_name varchar(128) NOT NULL,
    group_type varchar(32),
    remark varchar(512),
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_group PRIMARY KEY (id)
);
CREATE TABLE IF NOT EXISTS bre_group_member (
    id serial NOT NULL,
    group_id int,
    member_type varchar(16),
    member_id int,
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_group_member PRIMARY KEY (id),
    CONSTRAINT fk_group_member_group FOREIGN KEY (group_id) REFERENCES bre_group (id)
);
COMMENT ON TABLE bre_group IS '分组/标签（§3.5；family 虚拟组/category 复用）';

-- §3.6 育种报告（v1.7 进一期）
CREATE TABLE IF NOT EXISTS bre_report (
    id serial NOT NULL,
    report_name varchar(128) NOT NULL,
    report_type varchar(32),
    year int,
    target_id int,
    doc_path varchar(512),
    gen_by int,
    remark varchar(512),
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_report PRIMARY KEY (id)
);
COMMENT ON TABLE bre_report IS '育种报告（§3.6，docx/pdf 导出，v1.7 进一期）';

-- §3.7 分子基因型层（V2.0）
CREATE TABLE IF NOT EXISTS bre_marker (
    id serial NOT NULL,
    marker_name varchar(64) NOT NULL,
    chromosome varchar(16),
    position int,
    marker_type varchar(16),
    panel varchar(32),
    assembly_version varchar(32),
    remark varchar(512),
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_marker PRIMARY KEY (id),
    CONSTRAINT uq_bre_marker_name UNIQUE (marker_name)
);
CREATE TABLE IF NOT EXISTS bre_genotyping_dataset (
    id serial NOT NULL,
    dataset_name varchar(128) NOT NULL,
    platform varchar(32),
    panel varchar(32),
    purpose varchar(16),
    run_date date,
    lab varchar(128),
    remark varchar(512),
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_genotyping_dataset PRIMARY KEY (id)
);
CREATE TABLE IF NOT EXISTS bre_genotype_sample (
    id serial NOT NULL,
    dataset_id int,
    source_type varchar(16),
    source_id int,
    sample_type varchar(16),
    sample_date date,
    method varchar(64),
    lab varchar(128),
    remark varchar(512),
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_genotype_sample PRIMARY KEY (id),
    CONSTRAINT fk_genotype_sample_dataset FOREIGN KEY (dataset_id) REFERENCES bre_genotyping_dataset (id)
);
CREATE TABLE IF NOT EXISTS bre_genotype_call (
    id serial NOT NULL,
    sample_id int,
    marker_id int,
    allele varchar(32),
    remark varchar(256),
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_genotype_call PRIMARY KEY (id),
    CONSTRAINT fk_genotype_call_sample FOREIGN KEY (sample_id) REFERENCES bre_genotype_sample (id),
    CONSTRAINT fk_genotype_call_marker FOREIGN KEY (marker_id) REFERENCES bre_marker (id),
    CONSTRAINT uq_genotype_call_sample_marker UNIQUE (sample_id, marker_id)
);
COMMENT ON TABLE bre_marker IS '分子标记（§3.7；SSR/SNP，panel/assembly_version 供 GS 同版本）';
COMMENT ON TABLE bre_genotype_call IS '基因型调用（§3.7；allele 遵循 VCF/GP 0/1/2 编码）';

-- §3.8 克隆扩繁（P1，一期）
CREATE TABLE IF NOT EXISTS bre_propagation (
    id serial NOT NULL,
    batch_code varchar(64) NOT NULL,
    scion_source_type varchar(16),
    scion_source_id int,
    produced_germplasm_id int,
    rootstock_id int,
    method varchar(16),
    graft_date date,
    nursery_site_id int,
    operator_id int,
    scion_count int,
    grafted_count int,
    survival_count int,
    destination varchar(32),
    remark varchar(512),
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_propagation PRIMARY KEY (id),
    CONSTRAINT uq_bre_propagation_batch UNIQUE (batch_code),
    CONSTRAINT fk_propagation_germplasm FOREIGN KEY (produced_germplasm_id) REFERENCES bre_germplasm (id),
    CONSTRAINT fk_propagation_rootstock FOREIGN KEY (rootstock_id) REFERENCES bre_germplasm (id),
    CONSTRAINT fk_propagation_site FOREIGN KEY (nursery_site_id) REFERENCES bre_site (id),
    CONSTRAINT fk_propagation_operator FOREIGN KEY (operator_id) REFERENCES bre_personnel (id)
);
COMMENT ON TABLE bre_propagation IS '克隆扩繁批次（§3.8；入选株→克隆种质→扩繁→新树闭环）';

-- §3.9 环境因子（G×E 协变量）
CREATE TABLE IF NOT EXISTS bre_environment_condition (
    id serial NOT NULL,
    site_id int,
    year int,
    chilling_hours numeric(8,1),
    growing_degree_days numeric(8,1),
    rainfall_mm numeric(8,1),
    temp_avg numeric(6,1),
    soil_moisture numeric(6,1),
    source varchar(32),
    remark varchar(512),
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_environment_condition PRIMARY KEY (id),
    CONSTRAINT fk_env_site FOREIGN KEY (site_id) REFERENCES bre_site (id),
    CONSTRAINT uq_env_site_year UNIQUE (site_id, year)
);
COMMENT ON TABLE bre_environment_condition IS '环境因子（§3.9；G×E 协变量，site×year 唯一）';

-- §3.10 审计切面（通用，Service 写操作落）
CREATE TABLE IF NOT EXISTS bre_audit_log (
    id bigserial NOT NULL,
    entity_type varchar(32),
    entity_id int,
    action varchar(32),
    field_name varchar(64),
    old_value varchar(512),
    new_value varchar(512),
    operator_id int,
    created_time timestamptz NOT NULL DEFAULT now(),
    CONSTRAINT pk_bre_audit_log PRIMARY KEY (id),
    CONSTRAINT fk_audit_operator FOREIGN KEY (operator_id) REFERENCES bre_personnel (id)
);
COMMENT ON TABLE bre_audit_log IS '审计日志（§3.10；晋级审批/全程可追溯切面）';
CREATE INDEX IF NOT EXISTS ix_bre_audit_entity ON bre_audit_log (entity_type, entity_id);
CREATE INDEX IF NOT EXISTS ix_bre_audit_created ON bre_audit_log (created_time);

-- §3.11 选择规则（阈值/指数条件）
CREATE TABLE IF NOT EXISTS bre_selection_rule (
    id serial NOT NULL,
    rule_name varchar(128) NOT NULL,
    target_id int,
    stage varchar(32),
    conditions_json text NOT NULL,
    logic varchar(8) DEFAULT 'and',
    action varchar(16),
    priority int,
    enabled varchar(1) DEFAULT '1',
    remark varchar(512),
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_selection_rule PRIMARY KEY (id),
    CONSTRAINT fk_selection_rule_target FOREIGN KEY (target_id) REFERENCES bre_target (id)
);
COMMENT ON TABLE bre_selection_rule IS '选择规则（§3.11；conditions_json 阈值，可引用 trait_code/EBV）';

-- §3.12 育种值：模型元数据 + 值表（值表 V1.1 前移）
CREATE TABLE IF NOT EXISTS bre_prediction (
    id serial NOT NULL,
    model_name varchar(128),
    trait_id int,
    method varchar(32),
    accuracy numeric(5,3),
    train_n int,
    predict_date date,
    note varchar(512),
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_prediction PRIMARY KEY (id),
    CONSTRAINT fk_prediction_trait FOREIGN KEY (trait_id) REFERENCES bre_trait (id)
);
CREATE TABLE IF NOT EXISTS bre_prediction_value (
    id bigserial NOT NULL,
    prediction_id int,
    germplasm_id int,
    tree_id int,
    trait_id int,
    predicted_value numeric(12,4),
    reliability numeric(6,4),
    rank int,
    created_time timestamptz NOT NULL DEFAULT now(),
    CONSTRAINT pk_bre_prediction_value PRIMARY KEY (id),
    CONSTRAINT fk_prediction_value_prediction FOREIGN KEY (prediction_id) REFERENCES bre_prediction (id),
    CONSTRAINT fk_prediction_value_germplasm FOREIGN KEY (germplasm_id) REFERENCES bre_germplasm (id),
    CONSTRAINT fk_prediction_value_trait FOREIGN KEY (trait_id) REFERENCES bre_trait (id)
);
COMMENT ON TABLE bre_prediction IS '育种值模型/批次元数据（§3.12）';
COMMENT ON TABLE bre_prediction_value IS '个体预测值（EBV 持久化，V1.1 建表；趋势图/双轨选择/亲本决策读）';

-- §3.12 补充：配合力分析结果（GCA/SCA 持久化，一期落地）
CREATE TABLE IF NOT EXISTS bre_combining_ability (
    id serial NOT NULL,
    model_name varchar(128),
    trait_id int,
    method varchar(16),
    gca_json jsonb,
    sca_json jsonb,
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_combining_ability PRIMARY KEY (id),
    CONSTRAINT fk_combining_trait FOREIGN KEY (trait_id) REFERENCES bre_trait (id)
);
COMMENT ON TABLE bre_combining_ability IS '配合力分析结果（§3.12；GCA 按亲本、SCA 按组合，一期落地）';

-- §5 统计异步任务（R 引擎异步 job 队列）
CREATE TABLE IF NOT EXISTS bre_statistics_job (
    id bigserial NOT NULL,
    job_type varchar(32),
    params_json jsonb,
    status varchar(16) NOT NULL DEFAULT 'PENDING',
    result_ref int,
    error_msg text,
    started_time timestamptz,
    finished_time timestamptz,
    created_time timestamptz NOT NULL DEFAULT now(),
    created_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_statistics_job PRIMARY KEY (id)
);
COMMENT ON TABLE bre_statistics_job IS '统计异步任务（R 引擎；ABLUP/COMBINING 提交后异步执行并回写结果）';

-- §3.13 种子批（选择强度链前段）
CREATE TABLE IF NOT EXISTS bre_seed_lot (
    id serial NOT NULL,
    combination_id int,
    lot_code varchar(64) NOT NULL,
    harvest_year int,
    seed_count int,
    used_count int DEFAULT 0,
    germination_rate numeric(5,2),
    storage_type varchar(16),
    storage_location varchar(128),
    test_date date,
    remark varchar(512),
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_seed_lot PRIMARY KEY (id),
    CONSTRAINT uq_bre_seed_lot_code UNIQUE (lot_code),
    CONSTRAINT fk_seed_lot_combination FOREIGN KEY (combination_id) REFERENCES bre_cross_combination (id)
);
COMMENT ON TABLE bre_seed_lot IS '种子批（§3.13；used_count 派生 remaining，选择强度链源头）';

-- §3.14 试验处理（裂区/析因 factor×level）
CREATE TABLE IF NOT EXISTS bre_treatment (
    id serial NOT NULL,
    trial_study_id int,
    factor varchar(32) NOT NULL,
    level varchar(32) NOT NULL,
    description varchar(256),
    remark varchar(512),
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_treatment PRIMARY KEY (id),
    CONSTRAINT fk_treatment_study FOREIGN KEY (trial_study_id) REFERENCES bre_trial_study (id),
    CONSTRAINT uq_treatment_factor_level UNIQUE (trial_study_id, factor, level)
);
COMMENT ON TABLE bre_treatment IS '试验处理（§3.14；factor×level，BrAPI Treatment/MIAPPE ExperimentalFactor）';

-- §3.15 定植-处理关联（多对多）
CREATE TABLE IF NOT EXISTS bre_planting_treatment (
    id serial NOT NULL,
    planting_id int,
    treatment_id int,
    remark varchar(512),
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_planting_treatment PRIMARY KEY (id),
    CONSTRAINT fk_planting_treatment_planting FOREIGN KEY (planting_id) REFERENCES bre_planting (id),
    CONSTRAINT fk_planting_treatment_treatment FOREIGN KEY (treatment_id) REFERENCES bre_treatment (id),
    CONSTRAINT uq_planting_treatment UNIQUE (planting_id, treatment_id)
);
COMMENT ON TABLE bre_planting_treatment IS '定植-处理关联（§3.15；因子效应挂到 block 级批次全部 tree）';

-- §3.x 系谱管理（v1.9 补充；基于杂交组合自链 + 种质系谱串派生，独立维护亲子/世代关系）
CREATE TABLE IF NOT EXISTS bre_pedigree (
    id serial NOT NULL,
    combination_id int,
    child_code varchar(64),
    generation varchar(16),
    remark varchar(512),
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_pedigree PRIMARY KEY (id),
    CONSTRAINT fk_pedigree_combination FOREIGN KEY (combination_id) REFERENCES bre_cross_combination (id)
);
CREATE INDEX IF NOT EXISTS ix_bre_pedigree_created_deleted ON bre_pedigree (created_time, is_deleted);

-- §3.x 育种计划（v1.9 补充；顶层计划，germplasm.breeding_program 后续可升级为指向本表 FK）
CREATE TABLE IF NOT EXISTS bre_plan (
    id serial NOT NULL,
    plan_code varchar(64) NOT NULL,
    plan_name varchar(128) NOT NULL,
    objective varchar(512),
    start_year int,
    end_year int,
    leader varchar(64),
    remark varchar(512),
    created_time timestamptz NOT NULL DEFAULT now(),
    updated_time timestamptz,
    created_by int,
    updated_by int,
    is_deleted int NOT NULL DEFAULT 0,
    CONSTRAINT pk_bre_plan PRIMARY KEY (id),
    CONSTRAINT uq_bre_plan_code UNIQUE (plan_code)
);
CREATE INDEX IF NOT EXISTS ix_bre_plan_created_deleted ON bre_plan (created_time, is_deleted);

-- =====================================================================
-- 结构对齐补丁（V1.9 表 -> ModelMixin 基类契约）
-- 幂等，可重复执行：补齐 uuid / deleted_time，并将 is_deleted integer 改为 boolean。
-- 背景：v1.9 规格建表时遗漏 uuid/deleted_time 且 is_deleted 用 int，
--       而 _gen_specs 生成器产出的 model 继承 ModelMixin（要求这 3 列）。
-- =====================================================================
CREATE EXTENSION IF NOT EXISTS pgcrypto;

DO $$
DECLARE
    t text;
BEGIN
    FOREACH t IN ARRAY ARRAY[
        'bre_trait','bre_selection_rule','bre_trial',
        'bre_trial_study','bre_treatment','bre_group',
        'bre_pedigree','bre_plan'
    ] LOOP
        -- uuid（唯一）
        IF NOT EXISTS (
            SELECT 1 FROM information_schema.columns
            WHERE table_name = t AND column_name = 'uuid'
        ) THEN
            EXECUTE format('ALTER TABLE %I ADD COLUMN uuid varchar(64) NOT NULL DEFAULT gen_random_uuid()', t);
            EXECUTE format('CREATE UNIQUE INDEX IF NOT EXISTS uq_%I_uuid ON %I(uuid)', t, t);
        END IF;
        -- deleted_time（软删除时间，可空）
        IF NOT EXISTS (
            SELECT 1 FROM information_schema.columns
            WHERE table_name = t AND column_name = 'deleted_time'
        ) THEN
            EXECUTE format('ALTER TABLE %I ADD COLUMN deleted_time timestamptz', t);
        END IF;
        -- is_deleted: integer -> boolean
        IF EXISTS (
            SELECT 1 FROM information_schema.columns
            WHERE table_name = t AND column_name = 'is_deleted' AND data_type = 'integer'
        ) THEN
            EXECUTE format('ALTER TABLE %I ALTER COLUMN is_deleted DROP DEFAULT', t);
            EXECUTE format('ALTER TABLE %I ALTER COLUMN is_deleted TYPE boolean USING (is_deleted = 1)', t);
            EXECUTE format('ALTER TABLE %I ALTER COLUMN is_deleted SET DEFAULT false', t);
        END IF;
    END LOOP;
END $$;