147 lines
8.3 KiB
SQL
147 lines
8.3 KiB
SQL
-- GWAS/QTL/MAS 闭环（对应规格 §8.22）5 张新表。
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-- 全部幂等，可在已有 dev 库上重复执行。create_all 只建新表，本脚本显式补齐兜底。
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-- 2026-08-04
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-- ============ bre_gwas_result：GWAS 批次元数据 ============
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CREATE TABLE IF NOT EXISTS bre_gwas_result (
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id integer GENERATED BY DEFAULT AS IDENTITY PRIMARY KEY,
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dataset_id integer REFERENCES bre_genotyping_dataset(id) ON DELETE CASCADE,
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trait_id integer REFERENCES bre_trait(id) ON DELETE CASCADE,
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trait_code varchar(64),
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method varchar(16),
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n_individuals integer,
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n_markers integer,
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m_after_maf integer,
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maf_min numeric,
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n_pc integer,
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sig_level numeric,
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threshold_bonf numeric,
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n_sig_bonf integer,
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n_sig_fdr integer,
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n_qtl integer,
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data_version varchar(32),
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input_hash varchar(64),
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engine_version varchar(32),
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remark varchar(512),
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created_time timestamp with time zone NOT NULL DEFAULT now(),
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updated_time timestamp with time zone,
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is_deleted boolean NOT NULL DEFAULT false,
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deleted_time timestamp with time zone,
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created_id integer REFERENCES sys_user(id) ON UPDATE CASCADE ON DELETE SET NULL,
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updated_id integer REFERENCES sys_user(id) ON UPDATE CASCADE ON DELETE SET NULL,
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deleted_id integer REFERENCES sys_user(id) ON UPDATE CASCADE ON DELETE SET NULL,
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uuid varchar(64) NOT NULL
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);
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CREATE UNIQUE INDEX IF NOT EXISTS ix_bre_gwas_result_uuid ON bre_gwas_result (uuid);
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CREATE INDEX IF NOT EXISTS ix_bre_gwas_result_created_deleted ON bre_gwas_result (created_time, is_deleted);
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CREATE INDEX IF NOT EXISTS ix_bre_gwas_result_dataset_id ON bre_gwas_result (dataset_id);
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CREATE INDEX IF NOT EXISTS ix_bre_gwas_result_trait_id ON bre_gwas_result (trait_id);
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CREATE INDEX IF NOT EXISTS ix_bre_gwas_result_created_id ON bre_gwas_result (created_id);
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-- ============ bre_gwas_snp：逐标记关联结果 ============
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CREATE TABLE IF NOT EXISTS bre_gwas_snp (
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id integer GENERATED BY DEFAULT AS IDENTITY PRIMARY KEY,
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gwas_result_id integer NOT NULL REFERENCES bre_gwas_result(id) ON DELETE CASCADE,
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marker_id integer REFERENCES bre_marker(id) ON DELETE SET NULL,
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marker_name varchar(64),
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chromosome varchar(16),
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position integer,
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maf numeric,
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effect numeric,
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se numeric,
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t_value numeric,
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p_value numeric,
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neg_log10p numeric,
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q_value numeric,
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sig_bonf boolean,
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sig_fdr boolean,
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created_time timestamp with time zone NOT NULL DEFAULT now(),
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updated_time timestamp with time zone,
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is_deleted boolean NOT NULL DEFAULT false,
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deleted_time timestamp with time zone,
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created_id integer REFERENCES sys_user(id) ON UPDATE CASCADE ON DELETE SET NULL,
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updated_id integer REFERENCES sys_user(id) ON UPDATE CASCADE ON DELETE SET NULL,
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deleted_id integer REFERENCES sys_user(id) ON UPDATE CASCADE ON DELETE SET NULL,
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uuid varchar(64) NOT NULL
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);
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CREATE UNIQUE INDEX IF NOT EXISTS ix_bre_gwas_snp_uuid ON bre_gwas_snp (uuid);
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CREATE INDEX IF NOT EXISTS ix_bre_gwas_snp_created_deleted ON bre_gwas_snp (created_time, is_deleted);
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CREATE INDEX IF NOT EXISTS ix_bre_gwas_snp_gwas_result_id ON bre_gwas_snp (gwas_result_id);
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CREATE INDEX IF NOT EXISTS ix_bre_gwas_snp_marker_id ON bre_gwas_snp (marker_id);
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CREATE INDEX IF NOT EXISTS ix_bre_gwas_snp_created_id ON bre_gwas_snp (created_id);
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-- ============ bre_qtl：QTL 区间（known 人工 / gwas 自动） ============
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CREATE TABLE IF NOT EXISTS bre_qtl (
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id integer GENERATED BY DEFAULT AS IDENTITY PRIMARY KEY,
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trait_id integer REFERENCES bre_trait(id) ON DELETE CASCADE,
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chromosome varchar(16),
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start_bp integer,
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end_bp integer,
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peak_marker_id integer REFERENCES bre_marker(id) ON DELETE SET NULL,
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peak_marker_name varchar(64),
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peak_p numeric,
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n_markers integer,
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effect numeric,
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source varchar(8) DEFAULT 'known',
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gwas_result_id integer REFERENCES bre_gwas_result(id) ON DELETE CASCADE,
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remark varchar(512),
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created_time timestamp with time zone NOT NULL DEFAULT now(),
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updated_time timestamp with time zone,
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is_deleted boolean NOT NULL DEFAULT false,
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deleted_time timestamp with time zone,
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created_id integer REFERENCES sys_user(id) ON UPDATE CASCADE ON DELETE SET NULL,
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updated_id integer REFERENCES sys_user(id) ON UPDATE CASCADE ON DELETE SET NULL,
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deleted_id integer REFERENCES sys_user(id) ON UPDATE CASCADE ON DELETE SET NULL,
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uuid varchar(64) NOT NULL
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);
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CREATE UNIQUE INDEX IF NOT EXISTS ix_bre_qtl_uuid ON bre_qtl (uuid);
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CREATE INDEX IF NOT EXISTS ix_bre_qtl_created_deleted ON bre_qtl (created_time, is_deleted);
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CREATE INDEX IF NOT EXISTS ix_bre_qtl_trait_id ON bre_qtl (trait_id);
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CREATE INDEX IF NOT EXISTS ix_bre_qtl_peak_marker_id ON bre_qtl (peak_marker_id);
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CREATE INDEX IF NOT EXISTS ix_bre_qtl_created_id ON bre_qtl (created_id);
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-- ============ bre_mas_panel：MAS 标记辅助选择面板 ============
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CREATE TABLE IF NOT EXISTS bre_mas_panel (
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id integer GENERATED BY DEFAULT AS IDENTITY PRIMARY KEY,
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panel_name varchar(128),
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trait_id integer REFERENCES bre_trait(id) ON DELETE CASCADE,
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n_markers integer,
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remark varchar(512),
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created_time timestamp with time zone NOT NULL DEFAULT now(),
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updated_time timestamp with time zone,
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is_deleted boolean NOT NULL DEFAULT false,
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deleted_time timestamp with time zone,
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created_id integer REFERENCES sys_user(id) ON UPDATE CASCADE ON DELETE SET NULL,
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updated_id integer REFERENCES sys_user(id) ON UPDATE CASCADE ON DELETE SET NULL,
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deleted_id integer REFERENCES sys_user(id) ON UPDATE CASCADE ON DELETE SET NULL,
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uuid varchar(64) NOT NULL
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);
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CREATE UNIQUE INDEX IF NOT EXISTS ix_bre_mas_panel_uuid ON bre_mas_panel (uuid);
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CREATE INDEX IF NOT EXISTS ix_bre_mas_panel_created_deleted ON bre_mas_panel (created_time, is_deleted);
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CREATE INDEX IF NOT EXISTS ix_bre_mas_panel_trait_id ON bre_mas_panel (trait_id);
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CREATE INDEX IF NOT EXISTS ix_bre_mas_panel_created_id ON bre_mas_panel (created_id);
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-- ============ bre_mas_panel_marker：面板标记（唯一 panel+marker） ============
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CREATE TABLE IF NOT EXISTS bre_mas_panel_marker (
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id integer GENERATED BY DEFAULT AS IDENTITY PRIMARY KEY,
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panel_id integer NOT NULL REFERENCES bre_mas_panel(id) ON DELETE CASCADE,
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marker_id integer REFERENCES bre_marker(id) ON DELETE SET NULL,
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favorable_dose integer,
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effect numeric,
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direction varchar(8) DEFAULT 'high',
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created_time timestamp with time zone NOT NULL DEFAULT now(),
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updated_time timestamp with time zone,
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is_deleted boolean NOT NULL DEFAULT false,
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deleted_time timestamp with time zone,
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created_id integer REFERENCES sys_user(id) ON UPDATE CASCADE ON DELETE SET NULL,
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updated_id integer REFERENCES sys_user(id) ON UPDATE CASCADE ON DELETE SET NULL,
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deleted_id integer REFERENCES sys_user(id) ON UPDATE CASCADE ON DELETE SET NULL,
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uuid varchar(64) NOT NULL
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);
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CREATE UNIQUE INDEX IF NOT EXISTS ix_bre_mas_panel_marker_uuid ON bre_mas_panel_marker (uuid);
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CREATE UNIQUE INDEX IF NOT EXISTS uq_bre_mas_panel_marker_panel_marker ON bre_mas_panel_marker (panel_id, marker_id);
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CREATE INDEX IF NOT EXISTS ix_bre_mas_panel_marker_created_deleted ON bre_mas_panel_marker (created_time, is_deleted);
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CREATE INDEX IF NOT EXISTS ix_bre_mas_panel_marker_panel_id ON bre_mas_panel_marker (panel_id);
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CREATE INDEX IF NOT EXISTS ix_bre_mas_panel_marker_marker_id ON bre_mas_panel_marker (marker_id);
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CREATE INDEX IF NOT EXISTS ix_bre_mas_panel_marker_created_id ON bre_mas_panel_marker (created_id);
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