fix:java项目性能优化

README.md

@@ -9,9 +9,44 @@ This server implements all BrAPI calls. It is backed by a custom database with d
 Use [/calls](https://test-server.brapi.org/brapi/v1/call) (V1) or [/serverinfo](https://test-server.brapi.org/brapi/v2/serverinfo) (V2) to check the available endpoints.
 
 ## Prerequisites
-* Maven 3.9
+
-* Java 21
+| Tool | Required version | Notes |
-* Postgres 17.2
+| --- | --- | --- |
+| **Java (JDK)** | **21** (class file 65.0) | Compile **and** run must use JDK 21. Java 17 will fail at startup. |
+| **Maven** | **3.9.9+** | Used to build and run the backend. |
+| **PostgreSQL** | **17.2** | Empty schema; tables/data load on first startup. |
+
+This repo ships pinned tooling under `.tools/` (Windows-friendly):
+
+- JDK: `.tools/jdk-21.0.11+10` (Temurin 21.0.11)
+- Maven: `.tools/apache-maven-3.9.9`
+
+**PowerShell** (set env before `mvn`; do not use CMD `set` syntax in PowerShell):
+
+```powershell
+$env:JAVA_HOME = "D:\maimaiproject\brapi-java\.tools\jdk-21.0.11+10"
+$env:Path = "$env:JAVA_HOME\bin;" + $env:Path
+java -version   # should show 21.0.11
+mvn -version    # Java version should also be 21
+```
+
+**CMD**:
+
+```cmd
+set JAVA_HOME=D:\maimaiproject\brapi-java\.tools\jdk-21.0.11+10
+set Path=%JAVA_HOME%\bin;%Path%
+```
+
+Or use the bundled Maven directly:
+
+```powershell
+$env:JAVA_HOME = "D:\maimaiproject\brapi-java\.tools\jdk-21.0.11+10"
+$env:Path = "$env:JAVA_HOME\bin;" + $env:Path
+.\.tools\apache-maven-3.9.9\bin\mvn.cmd clean install
+.\.tools\apache-maven-3.9.9\bin\mvn.cmd spring-boot:run
+```
+
+Adjust the path if your checkout is not `D:\maimaiproject\brapi-java`.
 
 ## Auth Configuration
 BrAPI has provided a [sample central authentication service for the test server](https://brapi.org/oauth).

docs/dev/03-genotyping/06-variantset.md

@@ -31,9 +31,16 @@
 - VariantSet 列表页支持按 referenceSet、study、variantSetName 查询。
 - 详情页展示 variants、callsets、analysis、available formats。
 - 从 Study 工作台创建时默认带出 `study_id`。
+- **本版本不做**：单条删除、批量删除；放到下一版本实现。
 
 ## 关键校验
 
 1. `reference_set_id` 与下属 `variant.reference_set_id` 应保持一致。
-2. 删除 variantset 前检查 `variant`、`callset_variant_sets`、`variantset_analysis`、`variantset_format`。
+2. 导入大型 variantset 时建议先建 variantset，再异步导入 variants 和 calls。
-3. 导入大型 variantset 时建议先建 variantset，再异步导入 variants 和 calls。
+3. **下一版本再做**：删除 variantset 前检查 `variant`、`callset_variant_sets`、`variantset_analysis`、`variantset_format`（含单条删除与批量删除）。
+
+## 开发状态
+
+**已完成**（2026-05-28）：列表查询、新增、编辑、详情。
+
+**下一版本**：单条删除、批量删除。

docs/dev/03-genotyping/07-variant.md

@@ -47,11 +47,18 @@
 ## 页面与交互
 
 - Variant 列表页支持按 variantSet、referenceSet、variantName、variantType 查询。
-- 大批量位点建议通过文件导入，不建议普通表单逐条录入。
 - 详情页展示 allele_call 数量和 marker_position 入口。
+- **本版本不做**：单条删除、批量删除、大批量文件导入；放到下一版本实现。
+- 本版本仅支持少量位点的表单逐条录入；大批量位点导入下一版本再做。
 
 ## 关键校验
 
 1. `variant` 是位点定义，不能把样本 genotype 写在本表。
 2. `variant_set_id` 和 `reference_set_id` 应与所属 variantset 保持一致。
-3. 删除 variant 前检查 `allele_call` 和 `marker_position` 引用。
+3. **下一版本再做**：删除 variant 前检查 `allele_call` 和 `marker_position` 引用（含单条删除与批量删除）。
+
+## 开发状态
+
+**已完成**（2026-05-28）：列表查询、新增、编辑、详情。
+
+**下一版本**：单条删除、批量删除、大批量文件导入。

frontend/README.md

@@ -1,5 +1,9 @@
 # Frontend
 
+## Prerequisites
+
+Backend API proxy targets `http://localhost:8081` (see root [README](../README.md): **Java 21 + Maven 3.9.9**).
+
 ## Start
 
 ```bash

frontend/src/app/(app)/basic-dictionary/base/list/api.ts

@@ -109,7 +109,7 @@ export const mapListRecord = (list: ListSummary | ListDetails): ListRecord => ({
 });
 
 const toRequestBody = (payload: ListPayload, data?: string[]): ListNewRequest => ({
-  listName: requiredText(payload.listName ?? payload.list_name, "请填写列表名称"),
+  listName: requiredText(payload.listName ?? payload.list_name, "???????"),
   listType: requiredListType(payload.listType ?? payload.list_type),
   listDescription: optionalText(payload.listDescription ?? payload.list_description),
   listSource: optionalText(payload.listSource ?? payload.list_source),
@@ -119,7 +119,7 @@ const toRequestBody = (payload: ListPayload, data?: string[]): ListNewRequest =>
 });
 
 export async function fetchListRows(): Promise<ListRecord[]> {
-  const response = await request<BrapiListResponse<ListSummary>>("/brapi/v2/lists?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<ListSummary>>("/brapi/v2/lists?page=0&pageSize=10");
   return response.result.data.map(mapListRecord);
 }
 
@@ -129,7 +129,7 @@ export async function fetchListDetail(listDbId: string): Promise<ListRecord> {
 }
 
 export async function fetchPersonOptions(): Promise<SelectOption[]> {
-  const response = await request<BrapiListResponse<PersonResponse>>("/brapi/v2/people?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<PersonResponse>>("/brapi/v2/people?page=0&pageSize=10");
   return response.result.data.map((person) => {
     const name = [person.firstName, person.lastName].filter(Boolean).join(" ").trim();
     const label = name
@@ -199,7 +199,7 @@ export function normalizeNewItems(existing: string[], incoming: string[]): strin
     throw new Error(`以下列表项已存在：${duplicates.join("、")}`);
   }
   if (added.length === 0) {
-    throw new Error("请至少填写一个有效的列表项");
+    throw new Error("请至少填写一个有效的列表");
   }
   return added;
 }

frontend/src/app/(app)/basic-dictionary/base/location/api.ts

@@ -1,3 +1,4 @@
+import { DEFAULT_LIST_PAGE, DEFAULT_LIST_PAGE_SIZE } from "@/constants/api";
 import { getAuthToken } from "@/utils/token";
 import type { LocationRecord } from "@/services/dictionaryService";
 
@@ -29,7 +30,7 @@ async function request<T>(path: string, init?: RequestInit): Promise<T> {
 
   if (!response.ok) {
     const detail = await response.text();
-    throw new Error(detail || `请求失败：${response.status}`);
+    throw new Error(detail || `?????${response.status}`);
   }
   return response.json() as Promise<T>;
 }
@@ -63,7 +64,7 @@ const toRequestBody = (payload: LocationPayload) => ({
   topography: emptyToNull(payload.topography),
 });
 
-export async function fetchLocationRows(page = 0, pageSize = 1000): Promise<LocationRecord[]> {
+export async function fetchLocationRows(page = DEFAULT_LIST_PAGE, pageSize = DEFAULT_LIST_PAGE_SIZE): Promise<LocationRecord[]> {
   const response = await request<BrapiListResponse<Omit<LocationRecord, "id">>>(
     `/brapi/v2/locations?page=${encodeURIComponent(String(page))}&pageSize=${encodeURIComponent(String(pageSize))}`,
   );
@@ -79,7 +80,7 @@ export async function fetchLocationDetail(locationDbId: string): Promise<Locatio
 
 export async function createLocationRow(payload: LocationPayload): Promise<LocationRecord> {
   if (!emptyToNull(payload.locationName)) {
-    throw new Error("请填写地点名称");
+    throw new Error("???????");
   }
   const response = await request<BrapiListResponse<Omit<LocationRecord, "id">>>("/brapi/v2/locations", {
     method: "POST",
@@ -87,7 +88,7 @@ export async function createLocationRow(payload: LocationPayload): Promise<Locat
   });
   const location = response.result.data[0];
   if (!location) {
-    throw new Error("新增地点失败：后端未返回数据");
+    throw new Error("??????????????");
   }
   return mapLocation(location);
 }

frontend/src/app/(app)/basic-dictionary/ontology/api.ts

@@ -1,3 +1,4 @@
+import { DEFAULT_LIST_PAGE, DEFAULT_LIST_PAGE_SIZE } from "@/constants/api";
 import { getAuthToken } from "@/utils/token";
 import type { OntologyRecord } from "@/services/dictionaryService";
 
@@ -33,7 +34,7 @@ async function request<T>(path: string, init?: RequestInit): Promise<T> {
 
   if (!response.ok) {
     const detail = await response.text();
-    throw new Error(detail || `请求失败：${response.status}`);
+    throw new Error(detail || `?????${response.status}`);
   }
   return response.json() as Promise<T>;
 }
@@ -62,7 +63,7 @@ const toRequestBody = (payload: Record<string, unknown>): OntologyPayload => ({
   description: emptyToNull(payload.description),
 });
 
-export async function fetchOntologyRows(page = 0, pageSize = 1000): Promise<OntologyRecord[]> {
+export async function fetchOntologyRows(page = DEFAULT_LIST_PAGE, pageSize = DEFAULT_LIST_PAGE_SIZE): Promise<OntologyRecord[]> {
   const response = await request<BrapiListResponse<OntologyApiRecord>>(
     `/brapi/v2/ontologies?page=${encodeURIComponent(String(page))}&pageSize=${encodeURIComponent(String(pageSize))}`,
   );
@@ -79,7 +80,7 @@ export async function fetchOntologyDetail(ontologyDbId: string): Promise<Ontolog
 export async function createOntologyRow(payload: Record<string, unknown>): Promise<OntologyRecord> {
   const body = toRequestBody(payload);
   if (!body.ontologyName) {
-    throw new Error("请填写本体名称");
+    throw new Error("???????");
   }
   const response = await request<BrapiListResponse<OntologyApiRecord>>("/brapi/v2/ontologies", {
     method: "POST",
@@ -87,7 +88,7 @@ export async function createOntologyRow(payload: Record<string, unknown>): Promi
   });
   const ontology = response.result.data[0];
   if (!ontology) {
-    throw new Error("新增本体失败：后端未返回数据");
+    throw new Error("??????????????");
   }
   return mapOntology(ontology);
 }

frontend/src/app/(app)/basic-dictionary/trait-method-scale/api.ts

@@ -118,7 +118,7 @@ const compositeId = (kind: TraitMethodScaleKind, dbId: string) => `${kind}:${dbI
 const parseCompositeId = (id: string): { kind: TraitMethodScaleKind; dbId: string } => {
   const [kind, ...rest] = id.split(":");
   if (kind !== "Trait" && kind !== "Method" && kind !== "Scale") {
-    throw new Error("标准项类型无效");
+    throw new Error("标准项类型无");
   }
   return { kind, dbId: rest.join(":") };
 };
@@ -188,12 +188,12 @@ const payloadKind = (payload: TraitMethodScalePayload): TraitMethodScaleKind =>
 
 const commonName = (payload: TraitMethodScalePayload) => {
   const name = optionalText(payload.name);
-  if (!name) throw new Error("请填写名称");
+  if (!name) throw new Error("?????");
   return name;
 };
 
 export async function fetchOntologyOptions(): Promise<OntologyOption[]> {
-  const response = await request<BrapiListResponse<OntologyResponse>>("/brapi/v2/ontologies?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<OntologyResponse>>("/brapi/v2/ontologies?page=0&pageSize=10");
   return response.result.data.map((ontology) => ({
     value: ontology.ontologyDbId,
     label: `${ontology.ontologyName || ontology.ontology_name || ontology.ontologyDbId}${ontology.version ? ` / ${ontology.version}` : ""}`,
@@ -202,24 +202,24 @@ export async function fetchOntologyOptions(): Promise<OntologyOption[]> {
 
 export async function fetchTraitMethodScaleRows(kind?: TraitMethodScaleKind): Promise<TraitMethodScaleRecord[]> {
   if (kind === "Trait") {
-    const response = await request<BrapiListResponse<TraitResponse>>("/brapi/v2/traits?page=0&pageSize=1000");
+    const response = await request<BrapiListResponse<TraitResponse>>("/brapi/v2/traits?page=0&pageSize=10");
     return response.result.data.map(mapTrait);
   }
 
   if (kind === "Method") {
-    const response = await request<BrapiListResponse<MethodResponse>>("/brapi/v2/methods?page=0&pageSize=1000");
+    const response = await request<BrapiListResponse<MethodResponse>>("/brapi/v2/methods?page=0&pageSize=10");
     return response.result.data.map(mapMethod);
   }
 
   if (kind === "Scale") {
-    const response = await request<BrapiListResponse<ScaleResponse>>("/brapi/v2/scales?page=0&pageSize=1000");
+    const response = await request<BrapiListResponse<ScaleResponse>>("/brapi/v2/scales?page=0&pageSize=10");
     return response.result.data.map(mapScale);
   }
 
   const [traits, methods, scales] = await Promise.all([
-    request<BrapiListResponse<TraitResponse>>("/brapi/v2/traits?page=0&pageSize=1000"),
+    request<BrapiListResponse<TraitResponse>>("/brapi/v2/traits?page=0&pageSize=10"),
-    request<BrapiListResponse<MethodResponse>>("/brapi/v2/methods?page=0&pageSize=1000"),
+    request<BrapiListResponse<MethodResponse>>("/brapi/v2/methods?page=0&pageSize=10"),
-    request<BrapiListResponse<ScaleResponse>>("/brapi/v2/scales?page=0&pageSize=1000"),
+    request<BrapiListResponse<ScaleResponse>>("/brapi/v2/scales?page=0&pageSize=10"),
   ]);
 
   return [

frontend/src/app/(app)/genotyping/reference-set/api.ts

@@ -3,7 +3,10 @@ import { getAuthToken } from "@/utils/token";
 import {
   NONE_SELECT_VALUE,
   type ReferenceBasesRecord,
+  type ReferenceQuery,
   type ReferenceRecord,
+  type ReferenceSetPageOptions,
+  type ReferenceSetQuery,
   type ReferenceSetRecord,
   type SelectOption,
 } from "./types";
@@ -41,6 +44,11 @@ interface VariantSetResponse {
   referenceSetDbId: string | null;
 }
 
+interface VariantResponse {
+  variantDbId: string;
+  referenceSetDbId: string | null;
+}
+
 type ReferenceSetPayload = Partial<Record<
   | "id"
   | "reference_set_name"
@@ -86,7 +94,7 @@ async function request<T>(path: string, init?: RequestInit): Promise<T> {
 
   if (!response.ok) {
     const detail = await response.text();
-    throw new Error(detail || `Request failed: ${response.status}`);
+    throw new Error(detail || `请求失败：${response.status}`);
   }
   return response.json() as Promise<T>;
 }
@@ -105,7 +113,7 @@ const requiredText = (value: unknown, message: string) => {
 
 const optionalNumber = (value: unknown) => {
   const normalized = optionalText(value);
-  if (!normalized) return null;
+  if (normalized === null) return null;
   const parsed = Number(normalized);
   return Number.isNaN(parsed) ? null : parsed;
 };
@@ -125,19 +133,22 @@ const optionalUrl = (value: unknown, label: string) => {
   return normalized;
 };
 
-const validateBases = (value: unknown) => {
+const validateBases = (value: unknown, required = false) => {
   const normalized = optionalText(value);
-  if (!normalized) return null;
+  if (!normalized) {
+    if (required) throw new Error("碱基序列片段不能为空");
+    return null;
+  }
   if (normalized.length > 2048) {
     throw new Error("碱基序列片段不能超过 2048 字符");
   }
   if (!BASES_PATTERN.test(normalized)) {
-    throw new Error("碱基序列仅允许 A/C/G/T/N 及常见占位符");
+    throw new Error("碱基序列仅允<EFBFBD>?A/C/G/T/N 及常见占位符");
   }
   return normalized.toUpperCase();
 };
 
-const mapReferenceSet = (item: ReferenceSetRecord): ReferenceSetRecord => ({
+export const mapReferenceSet = (item: ReferenceSetRecord): ReferenceSetRecord => ({
   ...item,
   id: item.referenceSetDbId || item.id,
   reference_set_name: item.reference_set_name || item.referenceSetName || null,
@@ -166,7 +177,7 @@ const mapReferenceSet = (item: ReferenceSetRecord): ReferenceSetRecord => ({
     || null,
 });
 
-const mapReference = (reference: ReferenceRecord): ReferenceRecord => ({
+export const mapReference = (reference: ReferenceRecord): ReferenceRecord => ({
   ...reference,
   id: reference.referenceDbId || reference.id,
   reference_name: reference.reference_name || reference.referenceName || null,
@@ -175,7 +186,7 @@ const mapReference = (reference: ReferenceRecord): ReferenceRecord => ({
   source_divergence: reference.source_divergence ?? reference.sourceDivergence ?? null,
 });
 
-const mapReferenceBases = (item: ReferenceBasesRecord): ReferenceBasesRecord => ({
+export const mapReferenceBases = (item: ReferenceBasesRecord): ReferenceBasesRecord => ({
   ...item,
   id: item.referenceBasesDbId || item.id,
   reference_id: item.reference_id || item.referenceDbId || null,
@@ -183,63 +194,155 @@ const mapReferenceBases = (item: ReferenceBasesRecord): ReferenceBasesRecord =>
   page_number: item.page_number ?? item.pageNumber ?? null,
 });
 
-const referenceSetBody = (payload: ReferenceSetPayload) => ({
+function buildSpecies(payload: ReferenceSetPayload) {
-  referenceSetName: requiredText(payload.reference_set_name, "ReferenceSet 名称不能为空"),
+  const term = optionalText(payload.species_ontology_term);
-  assemblyPUI: optionalText(payload.assembly_pui),
+  const termURI = optionalUrl(payload.species_ontology_termuri, "物种本体 URI");
-  description: optionalText(payload.description),
+  if (!term && !termURI) return undefined;
-  isDerived: optionalBoolean(payload.is_derived),
+  return { term, termURI };
-  md5checksum: optionalText(payload.md5checksum),
+}
-  sourceURI: optionalUrl(payload.source_uri, "来源 URI"),
-  species: optionalText(payload.species_ontology_term) || optionalUrl(payload.species_ontology_termuri, "物种本体 URI")
-    ? {
-        term: optionalText(payload.species_ontology_term),
-        termURI: optionalUrl(payload.species_ontology_termuri, "物种本体 URI"),
-      }
-    : undefined,
-  sourceGermplasmDbId: optionalText(payload.source_germplasm_id),
-});
 
-const referenceBody = (payload: ReferencePayload) => ({
+function buildReferenceSetWriteBody(payload: ReferenceSetPayload) {
-  referenceName: requiredText(payload.reference_name, "Reference 名称不能为空"),
+  const body: Record<string, unknown> = {
-  referenceSetDbId: requiredText(payload.reference_set_id, "ReferenceSet 不能为空"),
+    referenceSetName: requiredText(payload.reference_set_name, "请填<EFBFBD>?ReferenceSet 名称"),
-  length: optionalNumber(payload.length),
+  };
-  md5checksum: optionalText(payload.md5checksum),
+  const optionalFields: Array<[string, unknown]> = [
-  sourceDivergence: optionalNumber(payload.source_divergence),
+    ["assemblyPUI", optionalText(payload.assembly_pui)],
-});
+    ["description", optionalText(payload.description)],
+    ["isDerived", optionalBoolean(payload.is_derived)],
+    ["md5checksum", optionalText(payload.md5checksum)],
+    ["sourceURI", optionalUrl(payload.source_uri, "来源 URI")],
+    ["sourceGermplasmDbId", optionalText(payload.source_germplasm_id)],
+  ];
+  optionalFields.forEach(([key, value]) => {
+    if (value !== null && value !== undefined) body[key] = value;
+  });
+  const species = buildSpecies(payload);
+  if (species) body.species = species;
+  return body;
+}
 
-const referenceBasesBody = (payload: ReferenceBasesPayload) => ({
+function buildReferenceWriteBody(payload: ReferencePayload) {
-  referenceDbId: requiredText(payload.reference_id, "Reference 不能为空"),
+  const body: Record<string, unknown> = {
-  pageNumber: optionalNumber(payload.page_number),
+    referenceName: requiredText(payload.reference_name, "请填<E8AFB7>?Reference 名称"),
-  bases: validateBases(payload.bases),
+    referenceSetDbId: requiredText(payload.reference_set_id, "请选择 ReferenceSet"),
-});
+  };
+  const length = optionalNumber(payload.length);
+  const sourceDivergence = optionalNumber(payload.source_divergence);
+  const md5checksum = optionalText(payload.md5checksum);
+  if (length !== null) {
+    if (length < 0) throw new Error("序列长度不能为负");
+    body.length = length;
+  }
+  if (sourceDivergence !== null) body.sourceDivergence = sourceDivergence;
+  if (md5checksum) body.md5checksum = md5checksum;
+  return body;
+}
 
-const attachReferenceSetCounts = (
+function buildReferenceBasesWriteBody(payload: ReferenceBasesPayload, creating: boolean) {
+  const pageNumber = optionalNumber(payload.page_number);
+  if (pageNumber === null) throw new Error("请填写分页序");
+  if (pageNumber < 0) throw new Error("分页序号不能为负");
+  return {
+    referenceDbId: requiredText(payload.reference_id, "请选择 Reference"),
+    pageNumber,
+    bases: validateBases(payload.bases, creating),
+  };
+}
+
+function filterReferenceSets(rows: ReferenceSetRecord[], query?: ReferenceSetQuery) {
+  const name = optionalText(query?.reference_set_name)?.toLowerCase();
+  const assembly = optionalText(query?.assembly_pui)?.toLowerCase();
+  return rows.filter((row) => {
+    if (name && !String(row.reference_set_name ?? "").toLowerCase().includes(name)) return false;
+    if (assembly && !String(row.assembly_pui ?? "").toLowerCase().includes(assembly)) return false;
+    return true;
+  });
+}
+
+function filterReferences(rows: ReferenceRecord[], query?: ReferenceQuery) {
+  const name = optionalText(query?.reference_name)?.toLowerCase();
+  const referenceSetId = optionalText(query?.reference_set_id);
+  return rows.filter((row) => {
+    if (referenceSetId && row.reference_set_id !== referenceSetId) return false;
+    if (name && !String(row.reference_name ?? "").toLowerCase().includes(name)) return false;
+    return true;
+  });
+}
+
+function attachReferenceSetCounts(
   rows: ReferenceSetRecord[],
   references: ReferenceRecord[],
   variantSets: VariantSetResponse[],
-) => rows.map((row) => ({
+  variants: VariantResponse[],
-  ...row,
+) {
-  reference_count: references.filter((item) => item.reference_set_id === row.id).length,
+  return rows.map((row) => ({
-  variantset_count: variantSets.filter((item) => item.referenceSetDbId === row.id).length,
+    ...row,
-}));
+    reference_count: references.filter((item) => item.reference_set_id === row.id).length,
+    variantset_count: variantSets.filter((item) => item.referenceSetDbId === row.id).length,
+    variant_count: variants.filter((item) => item.referenceSetDbId === row.id).length,
+  }));
+}
+
+function attachReferenceBasesStats(references: ReferenceRecord[], basesPages: ReferenceBasesRecord[]) {
+  return references.map((reference) => {
+    const pages = basesPages.filter((page) => page.reference_id === reference.id);
+    const basesTotalLength = pages.reduce((total, page) => total + String(page.bases ?? "").length, 0);
+    return {
+      ...reference,
+      bases_page_count: pages.length,
+      bases_total_length: basesTotalLength,
+    };
+  });
+}
+
+function enrichReferenceSetNames(
+  references: ReferenceRecord[],
+  referenceSets: ReferenceSetRecord[],
+): ReferenceRecord[] {
+  const label = new Map(referenceSets.map((item) => [item.id, item.reference_set_name || item.id]));
+  return references.map((reference) => ({
+    ...reference,
+    reference_set_name: reference.reference_set_id
+      ? label.get(reference.reference_set_id) ?? reference.reference_set_name
+      : reference.reference_set_name,
+  }));
+}
+
+function enrichGermplasmNames(
+  rows: ReferenceSetRecord[],
+  germplasm: SelectOption[],
+): ReferenceSetRecord[] {
+  const label = new Map(germplasm.map((item) => [item.value, item.label]));
+  return rows.map((row) => ({
+    ...row,
+    source_germplasm_name: row.source_germplasm_id
+      ? label.get(row.source_germplasm_id) ?? row.source_germplasm_name ?? row.source_germplasm_id
+      : row.source_germplasm_name,
+  }));
+}
 
 const referenceSetRowsLoader = createCachedLoader(async () => {
-  const response = await request<BrapiListResponse<ReferenceSetRecord>>("/brapi/v2/referencesets?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<ReferenceSetRecord>>("/brapi/v2/referencesets?page=0&pageSize=10");
   return response.result.data.map(mapReferenceSet);
 });
 
 const referenceRowsLoader = createCachedLoader(async () => {
-  const response = await request<BrapiListResponse<ReferenceRecord>>("/brapi/v2/references?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<ReferenceRecord>>("/brapi/v2/references?page=0&pageSize=10");
   return response.result.data.map(mapReference);
 });
 
 const variantSetRowsLoader = createCachedLoader(async () => {
-  const response = await request<BrapiListResponse<VariantSetResponse>>("/brapi/v2/variantsets?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<VariantSetResponse>>("/brapi/v2/variantsets?page=0&pageSize=10");
+  return response.result.data;
+});
+
+const variantRowsLoader = createCachedLoader(async () => {
+  const response = await request<BrapiListResponse<VariantResponse>>("/brapi/v2/variants?page=0&pageSize=10");
   return response.result.data;
 });
 
 const referenceBasesRowsLoader = createCachedLoader(async () => {
-  const response = await request<BrapiListResponse<ReferenceBasesRecord>>("/brapi/v2/referencebases?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<ReferenceBasesRecord>>("/brapi/v2/referencebases?page=0&pageSize=10");
   return response.result.data.map(mapReferenceBases);
 });
 
@@ -247,32 +350,11 @@ export function invalidateReferenceSetPageCache() {
   referenceSetRowsLoader.invalidate();
   referenceRowsLoader.invalidate();
   variantSetRowsLoader.invalidate();
+  variantRowsLoader.invalidate();
   referenceBasesRowsLoader.invalidate();
 }
 
-export async function fetchReferenceSetRows(force = false): Promise<ReferenceSetRecord[]> {
+export async function fetchReferenceSetOptions(force = false): Promise<ReferenceSetPageOptions> {
-  const [referenceSets, references, variantSets] = await Promise.all([
-    referenceSetRowsLoader.load(force),
-    referenceRowsLoader.load(force),
-    variantSetRowsLoader.load(force),
-  ]);
-
-  return attachReferenceSetCounts(referenceSets, references, variantSets);
-}
-
-export async function fetchReferenceRows(force = false): Promise<ReferenceRecord[]> {
-  return referenceRowsLoader.load(force);
-}
-
-export async function fetchReferenceBasesRows(force = false): Promise<ReferenceBasesRecord[]> {
-  return referenceBasesRowsLoader.load(force);
-}
-
-export async function fetchReferenceSetOptions(force = false): Promise<{
-  referenceSets: SelectOption[];
-  references: SelectOption[];
-  germplasm: SelectOption[];
-}> {
   const [sharedOptions, referenceSets, references] = await Promise.all([
     loadDropdownBundle({ germplasms: true }, force),
     referenceSetRowsLoader.load(force),
@@ -292,13 +374,127 @@ export async function fetchReferenceSetOptions(force = false): Promise<{
   };
 }
 
+export async function loadReferenceSetPageData(params: {
+  referenceSetQuery?: ReferenceSetQuery;
+  referenceQuery?: ReferenceQuery;
+  force?: boolean;
+} = {}) {
+  const force = params.force ?? false;
+  const [options, referenceSets, references, variantSets, variants, basesPages] = await Promise.all([
+    fetchReferenceSetOptions(force),
+    referenceSetRowsLoader.load(force),
+    referenceRowsLoader.load(force),
+    variantSetRowsLoader.load(force),
+    variantRowsLoader.load(force),
+    referenceBasesRowsLoader.load(force),
+  ]);
+
+  const enrichedSets = enrichGermplasmNames(
+    attachReferenceSetCounts(referenceSets, references, variantSets, variants),
+    options.germplasm,
+  );
+  const enrichedReferences = attachReferenceBasesStats(
+    enrichReferenceSetNames(references, referenceSets),
+    basesPages,
+  );
+
+  return {
+    options,
+    referenceSets: filterReferenceSets(enrichedSets, params.referenceSetQuery),
+    references: filterReferences(enrichedReferences, params.referenceQuery),
+    basesPages,
+    variantSets,
+    variants,
+  };
+}
+
+export async function fetchReferenceSetRows(query?: ReferenceSetQuery, force = false): Promise<ReferenceSetRecord[]> {
+  const { referenceSets } = await loadReferenceSetPageData({ referenceSetQuery: query, force });
+  return referenceSets;
+}
+
+export async function fetchReferenceRows(query?: ReferenceQuery, force = false): Promise<ReferenceRecord[]> {
+  const { references } = await loadReferenceSetPageData({ referenceQuery: query, force });
+  return references;
+}
+
+export async function fetchReferenceSetDetail(id: string): Promise<ReferenceSetRecord> {
+  const response = await request<BrapiSingleResponse<ReferenceSetRecord>>(
+    `/brapi/v2/referencesets/${encodeURIComponent(id)}`,
+  );
+  const { options, references, variantSets, variants } = await loadReferenceSetPageData();
+  const [detail] = enrichGermplasmNames(
+    attachReferenceSetCounts([mapReferenceSet(response.result)], references, variantSets, variants),
+    options.germplasm,
+  );
+  return detail;
+}
+
+export async function fetchReferenceDetail(id: string): Promise<ReferenceRecord> {
+  const response = await request<BrapiSingleResponse<ReferenceRecord>>(
+    `/brapi/v2/references/${encodeURIComponent(id)}`,
+  );
+  const { referenceSets, basesPages } = await loadReferenceSetPageData();
+  const [detail] = attachReferenceBasesStats(
+    enrichReferenceSetNames([mapReference(response.result)], referenceSets),
+    basesPages,
+  );
+  return detail;
+}
+
+export async function fetchReferenceBasesRows(referenceDbId?: string, force = false): Promise<ReferenceBasesRecord[]> {
+  const pages = await referenceBasesRowsLoader.load(force);
+  const filtered = referenceDbId
+    ? pages.filter((page) => page.reference_id === referenceDbId)
+    : pages;
+  return filtered.sort((a, b) => Number(a.page_number ?? 0) - Number(b.page_number ?? 0));
+}
+
+export function normalizeReferenceSetFormData(record: ReferenceSetRecord): Record<string, unknown> {
+  return {
+    id: record.id,
+    reference_set_name: record.reference_set_name ?? "",
+    assembly_pui: record.assembly_pui ?? "",
+    description: record.description ?? "",
+    is_derived: record.is_derived === true ? "true" : record.is_derived === false ? "false" : NONE_SELECT_VALUE,
+    md5checksum: record.md5checksum ?? "",
+    source_uri: record.source_uri ?? "",
+    species_ontology_term: record.species_ontology_term ?? "",
+    species_ontology_termuri: record.species_ontology_termuri ?? "",
+    source_germplasm_id: record.source_germplasm_id && record.source_germplasm_id !== NONE_SELECT_VALUE
+      ? record.source_germplasm_id
+      : NONE_SELECT_VALUE,
+  };
+}
+
+export function normalizeReferenceFormData(record: ReferenceRecord): Record<string, unknown> {
+  return {
+    id: record.id,
+    reference_name: record.reference_name ?? "",
+    reference_set_id: record.reference_set_id ?? "",
+    length: record.length ?? "",
+    md5checksum: record.md5checksum ?? "",
+    source_divergence: record.source_divergence ?? "",
+  };
+}
+
+export function normalizeReferenceBasesFormData(record: ReferenceBasesRecord): Record<string, unknown> {
+  return {
+    id: record.id,
+    reference_id: record.reference_id ?? "",
+    page_number: record.page_number ?? "",
+    bases: record.bases ?? "",
+  };
+}
+
 export async function createReferenceSetRow(payload: ReferenceSetPayload): Promise<ReferenceSetRecord> {
+  const body = {
+    ...buildReferenceSetWriteBody(payload),
+    ...(optionalText(payload.id) ? { referenceSetDbId: optionalText(payload.id) } : {}),
+  };
   const response = await request<BrapiListResponse<ReferenceSetRecord>>("/brapi/v2/referencesets", {
     method: "POST",
-    body: JSON.stringify({
+    body: JSON.stringify(body),
-      referenceSetDbId: requiredText(payload.id, "ReferenceSet ID 不能为空"),
-      ...referenceSetBody(payload),
-    }),
   });
   invalidateReferenceSetPageCache();
   return mapReferenceSet(response.result.data[0]);
@@ -313,7 +509,7 @@ export async function updateReferenceSetRow(id: string, payload: ReferenceSetPay
     `/brapi/v2/referencesets/${encodeURIComponent(id)}`,
     {
       method: "PUT",
-      body: JSON.stringify(referenceSetBody(payload)),
+      body: JSON.stringify(buildReferenceSetWriteBody(payload)),
     },
   );
   invalidateReferenceSetPageCache();
@@ -329,12 +525,13 @@ export async function deleteReferenceSetRow(id: string): Promise<void> {
 }
 
 export async function createReferenceRow(payload: ReferencePayload): Promise<ReferenceRecord> {
+  const body = {
+    ...buildReferenceWriteBody(payload),
+    ...(optionalText(payload.id) ? { referenceDbId: optionalText(payload.id) } : {}),
+  };
   const response = await request<BrapiListResponse<ReferenceRecord>>("/brapi/v2/references", {
     method: "POST",
-    body: JSON.stringify({
+    body: JSON.stringify(body),
-      referenceDbId: requiredText(payload.id, "Reference ID 不能为空"),
-      ...referenceBody(payload),
-    }),
   });
   invalidateReferenceSetPageCache();
   return mapReference(response.result.data[0]);
@@ -349,7 +546,7 @@ export async function updateReferenceRow(id: string, payload: ReferencePayload):
     `/brapi/v2/references/${encodeURIComponent(id)}`,
     {
       method: "PUT",
-      body: JSON.stringify(referenceBody(payload)),
+      body: JSON.stringify(buildReferenceWriteBody(payload)),
     },
   );
   invalidateReferenceSetPageCache();
@@ -365,12 +562,13 @@ export async function deleteReferenceRow(id: string): Promise<void> {
 }
 
 export async function createReferenceBasesRow(payload: ReferenceBasesPayload): Promise<ReferenceBasesRecord> {
+  const body = {
+    ...buildReferenceBasesWriteBody(payload, true),
+    ...(optionalText(payload.id) ? { referenceBasesDbId: optionalText(payload.id) } : {}),
+  };
   const response = await request<BrapiListResponse<ReferenceBasesRecord>>("/brapi/v2/referencebases", {
     method: "POST",
-    body: JSON.stringify({
+    body: JSON.stringify(body),
-      referenceBasesDbId: requiredText(payload.id, "ReferenceBases ID 不能为空"),
-      ...referenceBasesBody(payload),
-    }),
   });
   invalidateReferenceSetPageCache();
   return mapReferenceBases(response.result.data[0]);
@@ -385,7 +583,7 @@ export async function updateReferenceBasesRow(id: string, payload: ReferenceBase
     `/brapi/v2/referencebases/${encodeURIComponent(id)}`,
     {
       method: "PUT",
-      body: JSON.stringify(referenceBasesBody(payload)),
+      body: JSON.stringify(buildReferenceBasesWriteBody(payload, false)),
     },
   );
   invalidateReferenceSetPageCache();

frontend/src/app/(app)/genotyping/reference-set/components/ReferenceSetTab.tsx

@@ -0,0 +1,164 @@
+"use client";
+
+import Link from "next/link";
+import { useCallback, useMemo, useState } from "react";
+import { Layers, RotateCcw, Search } from "lucide-react";
+import { BrapiEntityPage, type BrapiFormField } from "@/components/brapi/BrapiEntityPage";
+import { Button } from "@/components/ui/button";
+import { Input } from "@/components/ui/input";
+import { Label } from "@/components/ui/label";
+import { Select, SelectContent, SelectItem, SelectTrigger, SelectValue } from "@/components/ui/select";
+import {
+  createReferenceSetRow,
+  deleteReferenceSetRow,
+  fetchReferenceSetDetail,
+  loadReferenceSetPageData,
+  normalizeReferenceSetFormData,
+  updateReferenceSetRow,
+} from "../api";
+import { boolLabel, optionOrNone, warnMd5Checksum } from "../referenceUtils";
+import { NONE_SELECT_VALUE, type ReferenceSetQuery, type SelectOption } from "../types";
+
+const booleanOptions: SelectOption[] = [
+  { value: NONE_SELECT_VALUE, label: "不指定" },
+  { value: "true", label: "是" },
+  { value: "false", label: "否" },
+];
+
+const emptyQuery = (): ReferenceSetQuery => ({
+  reference_set_name: "",
+  assembly_pui: "",
+});
+
+export function ReferenceSetTab() {
+  const [germplasmOptions, setGermplasmOptions] = useState<SelectOption[]>([]);
+  const [draftQuery, setDraftQuery] = useState<ReferenceSetQuery>(emptyQuery);
+  const [appliedQuery, setAppliedQuery] = useState<ReferenceSetQuery>(emptyQuery);
+
+  const loadRows = useCallback(async () => {
+    const { options, referenceSets } = await loadReferenceSetPageData({ referenceSetQuery: appliedQuery });
+    setGermplasmOptions(options.germplasm);
+    return referenceSets as unknown as Record<string, unknown>[];
+  }, [appliedQuery]);
+
+  const fetchRecord = useCallback(async (id: string) => {
+    const detail = await fetchReferenceSetDetail(id);
+    return normalizeReferenceSetFormData(detail);
+  }, []);
+
+  const fields = useMemo<BrapiFormField[]>(() => [
+    { key: "id", label: "ReferenceSet ID", type: "text", placeholder: "留空则系统自动生成（导入时可指定）" },
+    {
+      key: "reference_set_name",
+      label: "参考集合名称",
+      type: "text",
+      required: true,
+      placeholder: "如 Maize B73 v4",
+    },
+    { key: "assembly_pui", label: "Assembly PUI", type: "text", placeholder: "GA4GH 永久标识" },
+    { key: "description", label: "说明", type: "textarea", colSpan: 2, placeholder: "参考集合说明" },
+    { key: "is_derived", label: "是否派生参考", type: "select", options: booleanOptions },
+    { key: "md5checksum", label: "MD5 校验值", type: "text", placeholder: "32 位十六进制（建议）" },
+    { key: "source_uri", label: "来源 URI", type: "text", placeholder: "https://..." },
+    { key: "species_ontology_term", label: "物种本体 Term", type: "text", placeholder: "Zea mays" },
+    { key: "species_ontology_termuri", label: "物种本体 URI", type: "text", placeholder: "https://..." },
+    {
+      key: "source_germplasm_id",
+      label: "来源 Germplasm",
+      type: "select",
+      options: optionOrNone("不关联 Germplasm", germplasmOptions),
+    },
+  ], [germplasmOptions]);
+
+  const renderFormExtra = useCallback((props: { formData: Record<string, unknown> }) => {
+    const md5Warning = warnMd5Checksum(props.formData.md5checksum);
+    return (
+      <div className="col-span-2 space-y-2 rounded-lg border border-indigo-100 bg-indigo-50/60 p-3 text-xs text-indigo-900 dark:border-indigo-900/40 dark:bg-indigo-950/30 dark:text-indigo-100">
+        <p className="font-medium">校验说明</p>
+        <p>删除前服务端会检查是否仍被 Reference / VariantSet / Variant 引用。来源 Germplasm 必须已存在。</p>
+        {md5Warning ? <p className="text-amber-700 dark:text-amber-300">{md5Warning}</p> : null}
+      </div>
+    );
+  }, []);
+
+  const renderQueryForm = useCallback(() => (
+    <div className="rounded-xl border border-slate-200 bg-white p-4 dark:border-slate-800 dark:bg-slate-950">
+      <div className="grid gap-3 md:grid-cols-2">
+        <div className="space-y-1.5">
+          <Label className="text-xs text-slate-500">ReferenceSet 名称</Label>
+          <Input
+            value={draftQuery.reference_set_name ?? ""}
+            onChange={(event) => setDraftQuery((current) => ({ ...current, reference_set_name: event.target.value }))}
+            placeholder="名称模糊匹配"
+          />
+        </div>
+        <div className="space-y-1.5">
+          <Label className="text-xs text-slate-500">Assembly PUI</Label>
+          <Input
+            value={draftQuery.assembly_pui ?? ""}
+            onChange={(event) => setDraftQuery((current) => ({ ...current, assembly_pui: event.target.value }))}
+            placeholder="PUI 模糊匹配"
+          />
+        </div>
+      </div>
+      <div className="mt-3 flex justify-end gap-2">
+        <Button type="button" variant="outline" className="gap-2" onClick={() => { const reset = emptyQuery(); setDraftQuery(reset); setAppliedQuery(reset); }}>
+          <RotateCcw className="h-4 w-4" />
+          重置
+        </Button>
+        <Button type="button" className="gap-2" onClick={() => setAppliedQuery({ ...draftQuery })}>
+          <Search className="h-4 w-4" />
+          查询
+        </Button>
+      </div>
+    </div>
+  ), [draftQuery]);
+
+  return (
+    <BrapiEntityPage
+      useEnhancedDialog
+      icon={Layers}
+      iconBg="bg-gradient-to-br from-indigo-500 to-violet-600"
+      title="ReferenceSet 参考基因组集合"
+      description="维护参考基因组集合、Assembly 标识、物种信息与来源 Germplasm。点击进入详情可管理下属 Reference。"
+      addLabel="新增 ReferenceSet"
+      columns={[
+        {
+          key: "reference_set_name",
+          label: "名称",
+          render: (value, row) => {
+            const id = String(row.id ?? row.referenceSetDbId ?? "");
+            const name = String(value ?? "—");
+            if (!id) return name;
+            return (
+              <Link href={`/genotyping/reference-set/referencesets/${encodeURIComponent(id)}`} className="font-medium text-indigo-600 hover:underline dark:text-indigo-400">
+                {name}
+              </Link>
+            );
+          },
+        },
+        { key: "assembly_pui", label: "Assembly PUI" },
+        { key: "species_ontology_term", label: "物种" },
+        { key: "source_germplasm_name", label: "来源 Germplasm" },
+        { key: "reference_count", label: "Reference 数" },
+        { key: "variantset_count", label: "VariantSet 数" },
+        { key: "variant_count", label: "Variant 数" },
+        { key: "is_derived", label: "派生", render: boolLabel },
+      ]}
+      fields={fields}
+      data={[]}
+      stats={[{
+        label: "/brapi/v2/referencesets",
+        value: "BrAPI",
+        className: "bg-indigo-50 text-indigo-700 dark:bg-indigo-400/10 dark:text-indigo-200",
+      }]}
+      loadData={loadRows}
+      fetchRecord={fetchRecord}
+      createRecord={(payload) => createReferenceSetRow(payload) as unknown as Promise<Record<string, unknown>>}
+      updateRecord={(id, payload) => updateReferenceSetRow(id, payload) as unknown as Promise<Record<string, unknown>>}
+      deleteRecord={deleteReferenceSetRow}
+      renderQueryForm={() => renderQueryForm()}
+      renderFormExtra={renderFormExtra}
+    />
+  );
+}

frontend/src/app/(app)/genotyping/reference-set/components/ReferenceTab.tsx

@@ -0,0 +1,168 @@
+"use client";
+
+import Link from "next/link";
+import { useCallback, useMemo, useState } from "react";
+import { useSearchParams } from "next/navigation";
+import { BookOpen, RotateCcw, Search } from "lucide-react";
+import { BrapiEntityPage, type BrapiFormField } from "@/components/brapi/BrapiEntityPage";
+import { Button } from "@/components/ui/button";
+import { Input } from "@/components/ui/input";
+import { Label } from "@/components/ui/label";
+import { Select, SelectContent, SelectItem, SelectTrigger, SelectValue } from "@/components/ui/select";
+import {
+  createReferenceRow,
+  deleteReferenceRow,
+  fetchReferenceDetail,
+  loadReferenceSetPageData,
+  normalizeReferenceFormData,
+  updateReferenceRow,
+} from "../api";
+import { NONE_SELECT_VALUE, type ReferenceQuery, type SelectOption } from "../types";
+
+const emptyQuery = (): ReferenceQuery => ({
+  reference_name: "",
+  reference_set_id: NONE_SELECT_VALUE,
+});
+
+function toSelectValue(value: string | null | undefined) {
+  return value && value !== NONE_SELECT_VALUE ? value : NONE_SELECT_VALUE;
+}
+
+export function ReferenceTab() {
+  const searchParams = useSearchParams();
+  const [referenceSetOptions, setReferenceSetOptions] = useState<SelectOption[]>([]);
+  const [draftQuery, setDraftQuery] = useState<ReferenceQuery>(() => ({
+    ...emptyQuery(),
+    reference_set_id: searchParams.get("reference_set_id") ?? NONE_SELECT_VALUE,
+  }));
+  const [appliedQuery, setAppliedQuery] = useState<ReferenceQuery>(() => ({
+    ...emptyQuery(),
+    reference_set_id: searchParams.get("reference_set_id") ?? NONE_SELECT_VALUE,
+  }));
+
+  const urlDefaultFormValues = useMemo(() => {
+    const referenceSetId = searchParams.get("reference_set_id");
+    return referenceSetId ? { reference_set_id: referenceSetId } : undefined;
+  }, [searchParams]);
+
+  const loadRows = useCallback(async () => {
+    const { options, references } = await loadReferenceSetPageData({ referenceQuery: appliedQuery });
+    setReferenceSetOptions(options.referenceSets);
+    return references as unknown as Record<string, unknown>[];
+  }, [appliedQuery]);
+
+  const fetchRecord = useCallback(async (id: string) => {
+    const detail = await fetchReferenceDetail(id);
+    return normalizeReferenceFormData(detail);
+  }, []);
+
+  const fields = useMemo<BrapiFormField[]>(() => [
+    { key: "id", label: "Reference ID", type: "text", placeholder: "留空则系统自动生成（导入时可指定）" },
+    { key: "reference_name", label: "参考序列名称", type: "text", required: true, placeholder: "如 chr1" },
+    {
+      key: "reference_set_id",
+      label: "ReferenceSet",
+      type: "select",
+      required: true,
+      options: referenceSetOptions,
+    },
+    { key: "length", label: "序列长度", type: "number", placeholder: "非负整数" },
+    { key: "source_divergence", label: "来源差异度", type: "number", placeholder: "0.01" },
+    { key: "md5checksum", label: "MD5", type: "text", placeholder: "md5 checksum", colSpan: 2 },
+  ], [referenceSetOptions]);
+
+  const renderFormExtra = useCallback(() => (
+    <div className="col-span-2 rounded-lg border border-emerald-100 bg-emerald-50/60 p-3 text-xs text-emerald-900 dark:border-emerald-900/40 dark:bg-emerald-950/30 dark:text-emerald-100">
+      <p className="font-medium">校验说明</p>
+      <p>ReferenceSet 必选且必须存在。删除前服务端会检查 ReferenceBases 引用。详情页可维护序列分页。</p>
+    </div>
+  ), []);
+
+  const renderQueryForm = useCallback(() => (
+    <div className="rounded-xl border border-slate-200 bg-white p-4 dark:border-slate-800 dark:bg-slate-950">
+      <div className="grid gap-3 md:grid-cols-2">
+        <div className="space-y-1.5">
+          <Label className="text-xs text-slate-500">Reference 名称</Label>
+          <Input
+            value={draftQuery.reference_name ?? ""}
+            onChange={(event) => setDraftQuery((current) => ({ ...current, reference_name: event.target.value }))}
+            placeholder="名称模糊匹配"
+          />
+        </div>
+        <div className="space-y-1.5">
+          <Label className="text-xs text-slate-500">ReferenceSet</Label>
+          <Select
+            value={toSelectValue(draftQuery.reference_set_id)}
+            onValueChange={(value) => setDraftQuery((current) => ({ ...current, reference_set_id: value }))}
+          >
+            <SelectTrigger><SelectValue placeholder="全部" /></SelectTrigger>
+            <SelectContent>
+              <SelectItem value={NONE_SELECT_VALUE}>全部 ReferenceSet</SelectItem>
+              {referenceSetOptions.map((option) => (
+                <SelectItem key={option.value} value={option.value}>{option.label}</SelectItem>
+              ))}
+            </SelectContent>
+          </Select>
+        </div>
+      </div>
+      <div className="mt-3 flex justify-end gap-2">
+        <Button type="button" variant="outline" className="gap-2" onClick={() => { const reset = emptyQuery(); setDraftQuery(reset); setAppliedQuery(reset); }}>
+          <RotateCcw className="h-4 w-4" />
+          重置
+        </Button>
+        <Button type="button" className="gap-2" onClick={() => setAppliedQuery({ ...draftQuery })}>
+          <Search className="h-4 w-4" />
+          查询
+        </Button>
+      </div>
+    </div>
+  ), [draftQuery, referenceSetOptions]);
+
+  return (
+    <BrapiEntityPage
+      useEnhancedDialog
+      icon={BookOpen}
+      iconBg="bg-gradient-to-br from-emerald-500 to-teal-600"
+      title="Reference 参考序列"
+      description="维护染色体、Contig 或 Scaffold 等参考序列，隶属于 ReferenceSet。"
+      addLabel="新增 Reference"
+      defaultFormValues={urlDefaultFormValues}
+      columns={[
+        {
+          key: "reference_name",
+          label: "序列名称",
+          render: (value, row) => {
+            const id = String(row.id ?? row.referenceDbId ?? "");
+            const name = String(value ?? "—");
+            if (!id) return name;
+            return (
+              <Link href={`/genotyping/reference-set/references/${encodeURIComponent(id)}`} className="font-medium text-emerald-600 hover:underline dark:text-emerald-400">
+                {name}
+              </Link>
+            );
+          },
+        },
+        { key: "reference_set_name", label: "ReferenceSet" },
+        { key: "length", label: "长度" },
+        { key: "bases_page_count", label: "Bases 分页数" },
+        { key: "bases_total_length", label: "Bases 总长度" },
+        { key: "source_divergence", label: "来源差异" },
+        { key: "md5checksum", label: "MD5" },
+      ]}
+      fields={fields}
+      data={[]}
+      stats={[{
+        label: "/brapi/v2/references",
+        value: "BrAPI",
+        className: "bg-emerald-50 text-emerald-700 dark:bg-emerald-400/10 dark:text-emerald-200",
+      }]}
+      loadData={loadRows}
+      fetchRecord={fetchRecord}
+      createRecord={(payload) => createReferenceRow(payload) as unknown as Promise<Record<string, unknown>>}
+      updateRecord={(id, payload) => updateReferenceRow(id, payload) as unknown as Promise<Record<string, unknown>>}
+      deleteRecord={deleteReferenceRow}
+      renderQueryForm={() => renderQueryForm()}
+      renderFormExtra={renderFormExtra}
+    />
+  );
+}

frontend/src/app/(app)/genotyping/reference-set/page.tsx

@@ -1,159 +1,23 @@
 "use client";
 
-import { useCallback, useEffect, useMemo, useState } from "react";
+import { Suspense, useEffect, useState } from "react";
-import { BookOpen, Dna, Layers } from "lucide-react";
+import { useSearchParams } from "next/navigation";
-import { BrapiEntityPage, type BrapiFormField } from "@/components/brapi/BrapiEntityPage";
+import { BookOpen, Layers } from "lucide-react";
 import { Tabs, TabsContent, TabsList, TabsTrigger } from "@/components/ui/tabs";
-import {
+import { Skeleton } from "@/components/ui/skeleton";
-  createReferenceBasesRow,
+import { ReferenceSetTab } from "./components/ReferenceSetTab";
-  createReferenceRow,
+import { ReferenceTab } from "./components/ReferenceTab";
-  createReferenceSetRow,
-  deleteReferenceBasesRow,
-  deleteReferenceRow,
-  deleteReferenceSetRow,
-  fetchReferenceBasesRows,
-  fetchReferenceRows,
-  fetchReferenceSetOptions,
-  fetchReferenceSetRows,
-  updateReferenceBasesRow,
-  updateReferenceRow,
-  updateReferenceSetRow,
-} from "./api";
-import { NONE_SELECT_VALUE, type SelectOption } from "./types";
 
-const booleanOptions: SelectOption[] = [
+function ReferenceSetPageContent() {
-  { value: NONE_SELECT_VALUE, label: "不指定" },
+  const searchParams = useSearchParams();
-  { value: "true", label: "是" },
-  { value: "false", label: "否" },
-];
-
-const optionOrNone = (label: string, options: SelectOption[]) => [
-  { value: NONE_SELECT_VALUE, label },
-  ...options,
-];
-
-const boolLabel = (value: unknown) => {
-  if (value === true) return "是";
-  if (value === false) return "否";
-  return "N/A";
-};
-
-const truncateBases = (value: unknown) => {
-  const text = String(value ?? "").trim();
-  if (!text) return "N/A";
-  return text.length > 32 ? `${text.slice(0, 32)}…` : text;
-};
-
-export default function ReferenceSetPage() {
   const [tab, setTab] = useState("reference-sets");
-  const [referenceSetOptions, setReferenceSetOptions] = useState<SelectOption[]>([]);
-  const [referenceOptions, setReferenceOptions] = useState<SelectOption[]>([]);
-  const [germplasmOptions, setGermplasmOptions] = useState<SelectOption[]>([]);
-
-  const applyOptions = useCallback((options: Awaited<ReturnType<typeof fetchReferenceSetOptions>>) => {
-    setReferenceSetOptions(options.referenceSets);
-    setReferenceOptions(options.references);
-    setGermplasmOptions(options.germplasm);
-    return options;
-  }, []);
-
-  const refreshOptions = useCallback(async (force = false) => {
-    const options = await fetchReferenceSetOptions(force);
-    applyOptions(options);
-    return options;
-  }, [applyOptions]);
 
   useEffect(() => {
-    let mounted = true;
+    const nextTab = searchParams.get("tab");
-    refreshOptions()
+    if (nextTab === "references" || nextTab === "reference-sets") {
-      .catch(() => undefined)
+      setTab(nextTab);
-      .finally(() => {
+    }
-        if (!mounted) return;
+  }, [searchParams]);
-      });
-    return () => {
-      mounted = false;
-    };
-  }, [refreshOptions]);
-
-  const loadReferenceSets = useCallback(async () => {
-    const rows = await fetchReferenceSetRows();
-    return rows as unknown as Record<string, unknown>[];
-  }, []);
-
-  const loadReferences = useCallback(async () => {
-    const rows = await fetchReferenceRows();
-    return rows as unknown as Record<string, unknown>[];
-  }, []);
-
-  const loadReferenceBases = useCallback(async () => {
-    const rows = await fetchReferenceBasesRows();
-    return rows as unknown as Record<string, unknown>[];
-  }, []);
-
-  const refreshAfterMutation = useCallback(async <T,>(action: () => Promise<T>) => {
-    const result = await action();
-    await refreshOptions(true);
-    return result;
-  }, [refreshOptions]);
-
-  const referenceSetFields = useMemo<BrapiFormField[]>(() => [
-    { key: "id", label: "ReferenceSet ID", type: "text", required: true, placeholder: "refset-001" },
-    {
-      key: "reference_set_name",
-      label: "参考集合名称",
-      type: "text",
-      required: true,
-      placeholder: "Maize B73 v4",
-    },
-    { key: "assembly_pui", label: "Assembly PUI", type: "text", placeholder: "GA4GH 永久标识" },
-    { key: "description", label: "说明", type: "textarea", colSpan: 2, placeholder: "参考集合说明" },
-    { key: "is_derived", label: "是否派生参考", type: "select", options: booleanOptions },
-    { key: "md5checksum", label: "MD5 校验值", type: "text", placeholder: "md5 checksum" },
-    { key: "source_uri", label: "来源 URI", type: "text", placeholder: "https://..." },
-    { key: "species_ontology_term", label: "物种本体 Term", type: "text", placeholder: "Zea mays" },
-    { key: "species_ontology_termuri", label: "物种本体 URI", type: "text", placeholder: "https://..." },
-    {
-      key: "source_germplasm_id",
-      label: "来源 Germplasm",
-      type: "select",
-      options: optionOrNone("不关联 Germplasm", germplasmOptions),
-    },
-  ], [germplasmOptions]);
-
-  const referenceFields = useMemo<BrapiFormField[]>(() => [
-    { key: "id", label: "Reference ID", type: "text", required: true, placeholder: "reference-001" },
-    { key: "reference_name", label: "参考序列名称", type: "text", required: true, placeholder: "chr1" },
-    {
-      key: "reference_set_id",
-      label: "ReferenceSet",
-      type: "select",
-      required: true,
-      options: referenceSetOptions,
-    },
-    { key: "length", label: "序列长度", type: "number", placeholder: "1000000" },
-    { key: "source_divergence", label: "来源差异", type: "number", placeholder: "0.01" },
-    { key: "md5checksum", label: "MD5", type: "text", placeholder: "md5 checksum", colSpan: 2 },
-  ], [referenceSetOptions]);
-
-  const referenceBasesFields = useMemo<BrapiFormField[]>(() => [
-    { key: "id", label: "ReferenceBases ID", type: "text", required: true, placeholder: "refbases-001" },
-    {
-      key: "reference_id",
-      label: "Reference",
-      type: "select",
-      required: true,
-      options: referenceOptions,
-    },
-    { key: "page_number", label: "分页序号", type: "number", required: true, placeholder: "0" },
-    {
-      key: "bases",
-      label: "碱基序列片段",
-      type: "textarea",
-      required: true,
-      colSpan: 2,
-      placeholder: "ACGT...（最多 2048 字符）",
-    },
-  ], [referenceOptions]);
 
   return (
     <Tabs value={tab} onValueChange={setTab} className="flex min-h-full flex-col gap-4">
@@ -166,116 +30,31 @@ export default function ReferenceSetPage() {
           <BookOpen className="h-4 w-4" />
           Reference
         </TabsTrigger>
-        <TabsTrigger value="reference-bases" className="gap-2">
-          <Dna className="h-4 w-4" />
-          ReferenceBases
-        </TabsTrigger>
       </TabsList>
 
       {tab === "reference-sets" ? (
         <TabsContent value="reference-sets" className="mt-0 min-h-0 flex-1">
-          <BrapiEntityPage
+          <ReferenceSetTab />
-            useEnhancedDialog
-            icon={Layers}
-            iconBg="bg-gradient-to-br from-indigo-500 to-violet-600"
-            title="ReferenceSet 参考基因组集合"
-            description="维护参考基因组集合、Assembly 标识、物种信息和来源 Germplasm。"
-            addLabel="新增 ReferenceSet"
-            columns={[
-              { key: "referenceSetDbId", label: "ReferenceSet ID" },
-              { key: "reference_set_name", label: "名称" },
-              { key: "assembly_pui", label: "Assembly PUI" },
-              { key: "species_ontology_term", label: "物种" },
-              { key: "source_germplasm_name", label: "来源 Germplasm" },
-              { key: "reference_count", label: "Reference 数" },
-              { key: "variantset_count", label: "VariantSet 数" },
-              { key: "is_derived", label: "派生", render: boolLabel },
-            ]}
-            fields={referenceSetFields}
-            data={[]}
-            stats={[{
-              label: "/brapi/v2/referencesets",
-              value: "BrAPI",
-              className: "bg-indigo-50 text-indigo-700 dark:bg-indigo-400/10 dark:text-indigo-200",
-            }]}
-            loadData={loadReferenceSets}
-            createRecord={(payload) => refreshAfterMutation(() => createReferenceSetRow(payload)) as unknown as Promise<Record<string, unknown>>}
-            updateRecord={(id, payload) => refreshAfterMutation(() => updateReferenceSetRow(id, payload)) as unknown as Promise<Record<string, unknown>>}
-            deleteRecord={async (id) => {
-              await deleteReferenceSetRow(id);
-              await refreshOptions(true);
-            }}
-          />
         </TabsContent>
       ) : null}
 
       {tab === "references" ? (
         <TabsContent value="references" className="mt-0 min-h-0 flex-1">
-          <BrapiEntityPage
+          <ReferenceTab />
-            useEnhancedDialog
-            icon={BookOpen}
-            iconBg="bg-gradient-to-br from-emerald-500 to-teal-600"
-            title="Reference 参考序列"
-            description="维护 ReferenceSet 下的染色体、Contig 或 Scaffold 等参考序列。"
-            addLabel="新增 Reference"
-            columns={[
-              { key: "referenceDbId", label: "Reference ID" },
-              { key: "reference_name", label: "序列名称" },
-              { key: "reference_set_name", label: "ReferenceSet" },
-              { key: "length", label: "长度" },
-              { key: "source_divergence", label: "来源差异" },
-              { key: "md5checksum", label: "MD5" },
-            ]}
-            fields={referenceFields}
-            data={[]}
-            stats={[{
-              label: "/brapi/v2/references",
-              value: "BrAPI",
-              className: "bg-emerald-50 text-emerald-700 dark:bg-emerald-400/10 dark:text-emerald-200",
-            }]}
-            loadData={loadReferences}
-            createRecord={(payload) => refreshAfterMutation(() => createReferenceRow(payload)) as unknown as Promise<Record<string, unknown>>}
-            updateRecord={(id, payload) => refreshAfterMutation(() => updateReferenceRow(id, payload)) as unknown as Promise<Record<string, unknown>>}
-            deleteRecord={async (id) => {
-              await deleteReferenceRow(id);
-              await refreshOptions(true);
-            }}
-          />
-        </TabsContent>
-      ) : null}
-
-      {tab === "reference-bases" ? (
-        <TabsContent value="reference-bases" className="mt-0 min-h-0 flex-1">
-          <BrapiEntityPage
-            useEnhancedDialog
-            icon={Dna}
-            iconBg="bg-gradient-to-br from-cyan-500 to-blue-600"
-            title="ReferenceBases 序列片段"
-            description="按 Reference 分页维护碱基序列片段，适合导入或补录分页内容。"
-            addLabel="新增 ReferenceBases"
-            columns={[
-              { key: "referenceBasesDbId", label: "ID" },
-              { key: "reference_name", label: "Reference" },
-              { key: "page_number", label: "分页序号" },
-              { key: "bases", label: "碱基片段", render: truncateBases },
-            ]}
-            fields={referenceBasesFields}
-            data={[]}
-            stats={[{
-              label: "/brapi/v2/referencebases",
-              value: "Admin",
-              className: "bg-cyan-50 text-cyan-700 dark:bg-cyan-400/10 dark:text-cyan-200",
-            }]}
-            loadData={loadReferenceBases}
-            createRecord={(payload) => refreshAfterMutation(() => createReferenceBasesRow(payload)) as unknown as Promise<Record<string, unknown>>}
-            updateRecord={(id, payload) => refreshAfterMutation(() => updateReferenceBasesRow(id, payload)) as unknown as Promise<Record<string, unknown>>}
-            deleteRecord={async (id) => {
-              await deleteReferenceBasesRow(id);
-              await refreshOptions(true);
-            }}
-          />
         </TabsContent>
       ) : null}
     </Tabs>
   );
 }
+
+function PageFallback() {
+  return <Skeleton className="h-96 w-full rounded-xl" />;
+}
+
+export default function ReferenceSetPage() {
+  return (
+    <Suspense fallback={<PageFallback />}>
+      <ReferenceSetPageContent />
+    </Suspense>
+  );
+}

frontend/src/app/(app)/genotyping/reference-set/referenceUtils.ts

@@ -0,0 +1,38 @@
+import { NONE_SELECT_VALUE, type SelectOption } from "./types";
+
+export const MD5_PATTERN = /^[a-fA-F0-9]{32}$/;
+
+export function optionOrNone(label: string, options: SelectOption[]) {
+  return [{ value: NONE_SELECT_VALUE, label }, ...options];
+}
+
+export function optionLabel(options: SelectOption[], value: unknown) {
+  const text = String(value ?? "").trim();
+  if (!text || text === NONE_SELECT_VALUE) return "—";
+  return options.find((option) => option.value === text)?.label || text;
+}
+
+export function boolLabel(value: unknown) {
+  if (value === true || value === "true") return "是";
+  if (value === false || value === "false") return "否";
+  return "—";
+}
+
+export function truncateText(value: unknown, max = 32) {
+  const text = String(value ?? "").trim();
+  if (!text) return "—";
+  return text.length > max ? `${text.slice(0, max)}…` : text;
+}
+
+export function warnMd5Checksum(value: unknown) {
+  const normalized = String(value ?? "").trim();
+  if (!normalized) return null;
+  if (!MD5_PATTERN.test(normalized)) {
+    return "MD5 建议为 32 位十六进制，当前格式可能不规范（不阻断保存）";
+  }
+  return null;
+}
+
+export function sumBasesLength(pages: Array<{ bases?: string | null }>) {
+  return pages.reduce((total, page) => total + String(page.bases ?? "").length, 0);
+}

frontend/src/app/(app)/genotyping/reference-set/references/[referenceDbId]/page.tsx

@@ -0,0 +1,165 @@
+"use client";
+
+import Link from "next/link";
+import { useCallback, useEffect, useMemo, useState } from "react";
+import { useParams } from "next/navigation";
+import { ArrowLeft, BookOpen, Dna } from "lucide-react";
+import { BrapiEntityPage, type BrapiFormField } from "@/components/brapi/BrapiEntityPage";
+import { Badge } from "@/components/ui/badge";
+import { Button } from "@/components/ui/button";
+import { Card, CardContent, CardHeader, CardTitle } from "@/components/ui/card";
+import { Skeleton } from "@/components/ui/skeleton";
+import {
+  createReferenceBasesRow,
+  deleteReferenceBasesRow,
+  fetchReferenceBasesRows,
+  fetchReferenceDetail,
+  normalizeReferenceBasesFormData,
+  updateReferenceBasesRow,
+} from "../../api";
+import { truncateText } from "../../referenceUtils";
+import type { ReferenceRecord } from "../../types";
+
+export default function ReferenceDetailPage() {
+  const params = useParams<{ referenceDbId: string }>();
+  const referenceDbId = decodeURIComponent(params.referenceDbId);
+
+  const [loading, setLoading] = useState(true);
+  const [error, setError] = useState<string | null>(null);
+  const [detail, setDetail] = useState<ReferenceRecord | null>(null);
+
+  useEffect(() => {
+    let mounted = true;
+    setLoading(true);
+    setError(null);
+    fetchReferenceDetail(referenceDbId)
+      .then((record) => {
+        if (!mounted) return;
+        setDetail(record);
+      })
+      .catch((event) => {
+        if (!mounted) return;
+        setError(event instanceof Error ? event.message : "加载 Reference 详情失败");
+      })
+      .finally(() => {
+        if (mounted) setLoading(false);
+      });
+    return () => { mounted = false; };
+  }, [referenceDbId]);
+
+  const defaultFormValues = useMemo(() => ({ reference_id: referenceDbId }), [referenceDbId]);
+
+  const loadBases = useCallback(async () => {
+    const rows = await fetchReferenceBasesRows(referenceDbId);
+    return rows as unknown as Record<string, unknown>[];
+  }, [referenceDbId]);
+
+  const fetchRecord = useCallback(async (id: string) => {
+    const rows = await fetchReferenceBasesRows(referenceDbId);
+    const found = rows.find((row) => row.id === id);
+    if (!found) throw new Error("ReferenceBases 记录不存在");
+    return normalizeReferenceBasesFormData({ ...found, reference_id: referenceDbId });
+  }, [referenceDbId]);
+
+  const fields = useMemo<BrapiFormField[]>(() => [
+    { key: "id", label: "ReferenceBases ID", type: "text", placeholder: "留空则系统自动生成" },
+    { key: "page_number", label: "分页序号", type: "number", required: true, placeholder: "0 起" },
+    {
+      key: "bases",
+      label: "碱基序列片段",
+      type: "textarea",
+      required: true,
+      colSpan: 2,
+      placeholder: "ACGT...（最多 2048 字符，建议文件导入）",
+    },
+  ], []);
+
+  const lengthMismatch = detail?.length != null
+    && detail.bases_total_length != null
+    && Number(detail.length) > 0
+    && Number(detail.bases_total_length) !== Number(detail.length);
+
+  if (loading) {
+    return (
+      <div className="space-y-4 p-1">
+        <Skeleton className="h-10 w-48" />
+        <Skeleton className="h-36 w-full" />
+        <Skeleton className="h-96 w-full" />
+      </div>
+    );
+  }
+
+  if (error || !detail) {
+    return (
+      <div className="rounded-xl border border-destructive/20 bg-destructive/10 px-4 py-6 text-sm text-destructive">
+        {error || "Reference 不存在"}
+        <div className="mt-4">
+          <Button asChild variant="outline">
+            <Link href="/genotyping/reference-set"><ArrowLeft className="mr-2 h-4 w-4" />返回列表</Link>
+          </Button>
+        </div>
+      </div>
+    );
+  }
+
+  return (
+    <div className="flex min-h-full flex-col gap-4">
+      <Button asChild variant="outline" size="sm" className="w-fit">
+        <Link href={detail.reference_set_id ? `/genotyping/reference-set/referencesets/${encodeURIComponent(detail.reference_set_id)}` : "/genotyping/reference-set"}>
+          <ArrowLeft className="mr-2 h-4 w-4" />
+          返回 ReferenceSet
+        </Link>
+      </Button>
+
+      <Card>
+        <CardHeader className="pb-3">
+          <CardTitle className="flex items-center gap-2 text-lg">
+            <BookOpen className="h-5 w-5 text-emerald-500" />
+            {detail.reference_name || detail.id}
+          </CardTitle>
+        </CardHeader>
+        <CardContent className="grid gap-3 text-sm sm:grid-cols-2 lg:grid-cols-4">
+          <div><span className="text-slate-500">Reference ID：</span>{detail.id}</div>
+          <div><span className="text-slate-500">ReferenceSet：</span>{detail.reference_set_name || detail.reference_set_id || "—"}</div>
+          <div><span className="text-slate-500">序列长度：</span>{detail.length ?? "—"}</div>
+          <div><span className="text-slate-500">MD5：</span>{detail.md5checksum || "—"}</div>
+          <div><span className="text-slate-500">来源差异：</span>{detail.source_divergence ?? "—"}</div>
+          <div><span className="text-slate-500">Bases 分页数：</span>{detail.bases_page_count ?? 0}</div>
+          <div><span className="text-slate-500">Bases 总长度：</span>{detail.bases_total_length ?? 0}</div>
+        </CardContent>
+      </Card>
+
+      {lengthMismatch ? (
+        <Badge variant="outline" className="w-fit border-amber-200 bg-amber-50 text-amber-800 dark:border-amber-900 dark:bg-amber-950 dark:text-amber-200">
+          Bases 总长度 ({detail.bases_total_length}) 与声明长度 ({detail.length}) 不一致，请检查分页数据
+        </Badge>
+      ) : null}
+
+      <BrapiEntityPage
+        useEnhancedDialog
+        icon={Dna}
+        iconBg="bg-gradient-to-br from-cyan-500 to-blue-600"
+        title="ReferenceBases 序列分页"
+        description="按 page_number 维护碱基片段；长序列建议走文件导入，不建议手工逐页录入。"
+        addLabel="新增分页"
+        defaultFormValues={defaultFormValues}
+        columns={[
+          { key: "page_number", label: "分页序号" },
+          { key: "bases", label: "碱基片段", render: (value) => truncateText(value) },
+        ]}
+        fields={fields}
+        data={[]}
+        stats={[{
+          label: "/brapi/v2/referencebases",
+          value: "Admin",
+          className: "bg-cyan-50 text-cyan-700 dark:bg-cyan-400/10 dark:text-cyan-200",
+        }]}
+        loadData={loadBases}
+        fetchRecord={fetchRecord}
+        createRecord={(payload) => createReferenceBasesRow({ ...payload, reference_id: referenceDbId }) as unknown as Promise<Record<string, unknown>>}
+        updateRecord={(id, payload) => updateReferenceBasesRow(id, { ...payload, reference_id: referenceDbId }) as unknown as Promise<Record<string, unknown>>}
+        deleteRecord={deleteReferenceBasesRow}
+      />
+    </div>
+  );
+}

frontend/src/app/(app)/genotyping/reference-set/referencesets/[referenceSetDbId]/page.tsx

@@ -0,0 +1,148 @@
+"use client";
+
+import Link from "next/link";
+import { useCallback, useEffect, useMemo, useState } from "react";
+import { useParams } from "next/navigation";
+import { ArrowLeft, BookOpen, Layers, Sigma } from "lucide-react";
+import { BrapiEntityPage, type BrapiFormField } from "@/components/brapi/BrapiEntityPage";
+import { Button } from "@/components/ui/button";
+import { Card, CardContent, CardHeader, CardTitle } from "@/components/ui/card";
+import { Skeleton } from "@/components/ui/skeleton";
+import {
+  fetchReferenceRows,
+  fetchReferenceSetDetail,
+} from "../../api";
+import { boolLabel } from "../../referenceUtils";
+import type { ReferenceRecord, ReferenceSetRecord } from "../../types";
+
+export default function ReferenceSetDetailPage() {
+  const params = useParams<{ referenceSetDbId: string }>();
+  const referenceSetDbId = decodeURIComponent(params.referenceSetDbId);
+
+  const [loading, setLoading] = useState(true);
+  const [error, setError] = useState<string | null>(null);
+  const [detail, setDetail] = useState<ReferenceSetRecord | null>(null);
+
+  useEffect(() => {
+    let mounted = true;
+    setLoading(true);
+    setError(null);
+    fetchReferenceSetDetail(referenceSetDbId)
+      .then((record) => {
+        if (!mounted) return;
+        setDetail(record);
+      })
+      .catch((event) => {
+        if (!mounted) return;
+        setError(event instanceof Error ? event.message : "加载 ReferenceSet 详情失败");
+      })
+      .finally(() => {
+        if (mounted) setLoading(false);
+      });
+    return () => { mounted = false; };
+  }, [referenceSetDbId]);
+
+  const loadReferences = useCallback(async () => {
+    const rows = await fetchReferenceRows({ reference_set_id: referenceSetDbId });
+    return rows as unknown as Record<string, unknown>[];
+  }, [referenceSetDbId]);
+
+  const referenceColumns = useMemo(() => [
+    {
+      key: "reference_name",
+      label: "序列名称",
+      render: (value: unknown, row: Record<string, unknown>) => {
+        const id = String(row.id ?? row.referenceDbId ?? "");
+        const name = String(value ?? "—");
+        if (!id) return name;
+        return (
+          <Link href={`/genotyping/reference-set/references/${encodeURIComponent(id)}`} className="font-medium text-emerald-600 hover:underline dark:text-emerald-400">
+            {name}
+          </Link>
+        );
+      },
+    },
+    { key: "length", label: "长度" },
+    { key: "bases_page_count", label: "Bases 分页数" },
+    { key: "md5checksum", label: "MD5" },
+  ], []);
+
+  const emptyFields = useMemo<BrapiFormField[]>(() => [], []);
+
+  if (loading) {
+    return (
+      <div className="space-y-4 p-1">
+        <Skeleton className="h-10 w-48" />
+        <Skeleton className="h-36 w-full" />
+        <Skeleton className="h-96 w-full" />
+      </div>
+    );
+  }
+
+  if (error || !detail) {
+    return (
+      <div className="rounded-xl border border-destructive/20 bg-destructive/10 px-4 py-6 text-sm text-destructive">
+        {error || "ReferenceSet 不存在"}
+        <div className="mt-4">
+          <Button asChild variant="outline">
+            <Link href="/genotyping/reference-set"><ArrowLeft className="mr-2 h-4 w-4" />返回列表</Link>
+          </Button>
+        </div>
+      </div>
+    );
+  }
+
+  return (
+    <div className="flex min-h-full flex-col gap-4">
+      <Button asChild variant="outline" size="sm" className="w-fit">
+        <Link href="/genotyping/reference-set"><ArrowLeft className="mr-2 h-4 w-4" />返回 ReferenceSet 列表</Link>
+      </Button>
+
+      <Card>
+        <CardHeader className="pb-3">
+          <CardTitle className="flex items-center gap-2 text-lg">
+            <Layers className="h-5 w-5 text-indigo-500" />
+            {detail.reference_set_name || detail.id}
+          </CardTitle>
+        </CardHeader>
+        <CardContent className="grid gap-3 text-sm sm:grid-cols-2 lg:grid-cols-4">
+          <div><span className="text-slate-500">ReferenceSet ID：</span>{detail.id}</div>
+          <div><span className="text-slate-500">Assembly PUI：</span>{detail.assembly_pui || "—"}</div>
+          <div><span className="text-slate-500">物种：</span>{detail.species_ontology_term || "—"}</div>
+          <div><span className="text-slate-500">来源 Germplasm：</span>{detail.source_germplasm_name || "—"}</div>
+          <div><span className="text-slate-500">Reference 数：</span>{detail.reference_count ?? 0}</div>
+          <div><span className="text-slate-500">VariantSet 数：</span>{detail.variantset_count ?? 0}</div>
+          <div><span className="text-slate-500">Variant 数：</span>{detail.variant_count ?? 0}</div>
+          <div><span className="text-slate-500">派生参考：</span>{boolLabel(detail.is_derived)}</div>
+          <div className="sm:col-span-2"><span className="text-slate-500">说明：</span>{detail.description || "—"}</div>
+        </CardContent>
+      </Card>
+
+      <div className="flex flex-wrap gap-2">
+        <Button asChild variant="outline" size="sm">
+          <Link href={`/genotyping/reference-set?tab=references&reference_set_id=${encodeURIComponent(detail.id)}`}>
+            <BookOpen className="mr-2 h-4 w-4" />
+            在 Reference 列表中查看
+          </Link>
+        </Button>
+        <Button asChild variant="outline" size="sm">
+          <Link href="/genotyping/variant">
+            <Sigma className="mr-2 h-4 w-4" />
+            前往 Variant / VariantSet
+          </Link>
+        </Button>
+      </div>
+
+      <BrapiEntityPage
+        icon={BookOpen}
+        iconBg="bg-gradient-to-br from-emerald-500 to-teal-600"
+        title="下属 Reference"
+        description="该 ReferenceSet 下的参考序列列表，点击名称进入 Reference 详情维护 Bases。"
+        columns={referenceColumns}
+        fields={emptyFields}
+        data={[]}
+        loadData={loadReferences}
+      />
+    </div>
+  );
+}

frontend/src/app/(app)/genotyping/reference-set/types.ts

@@ -5,6 +5,16 @@ export interface SelectOption {
   label: string;
 }
 
+export interface ReferenceSetQuery {
+  reference_set_name?: string;
+  assembly_pui?: string;
+}
+
+export interface ReferenceQuery {
+  reference_name?: string;
+  reference_set_id?: string;
+}
+
 export interface ReferenceSetRecord {
   id: string;
   referenceSetDbId: string;
@@ -28,6 +38,7 @@ export interface ReferenceSetRecord {
   source_germplasm_name: string | null;
   reference_count?: number | null;
   variantset_count?: number | null;
+  variant_count?: number | null;
 }
 
 export interface ReferenceRecord {
@@ -43,6 +54,8 @@ export interface ReferenceRecord {
   md5checksum: string | null;
   sourceDivergence: number | string | null;
   source_divergence: number | string | null;
+  bases_page_count?: number | null;
+  bases_total_length?: number | null;
 }
 
 export interface ReferenceBasesRecord {
@@ -56,3 +69,9 @@ export interface ReferenceBasesRecord {
   pageNumber: number | string | null;
   bases: string | null;
 }
+
+export interface ReferenceSetPageOptions {
+  referenceSets: SelectOption[];
+  references: SelectOption[];
+  germplasm: SelectOption[];
+}

frontend/src/app/(app)/genotyping/sample-plate/api.ts

@@ -143,7 +143,7 @@ async function request<T>(path: string, init?: RequestInit): Promise<T> {
 
   if (!response.ok) {
     const detail = await response.text();
-    throw new Error(detail || `请求失败：${response.status}`);
+    throw new Error(detail || `?????${response.status}`);
   }
   return response.json() as Promise<T>;
 }
@@ -168,7 +168,7 @@ const optionalNumber = (value: unknown) => {
 };
 
 const trialContextLoader = createCachedLoader(async () => {
-  const response = await request<BrapiListResponse<TrialResponse>>("/brapi/v2/trials?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<TrialResponse>>("/brapi/v2/trials?page=0&pageSize=10");
   return response.result.data.map((trial) => ({
     value: trial.trialDbId,
     label: trial.trialName || trial.trialDbId,
@@ -177,7 +177,7 @@ const trialContextLoader = createCachedLoader(async () => {
 });
 
 const studyContextLoader = createCachedLoader(async () => {
-  const response = await request<BrapiListResponse<StudyResponse>>("/brapi/v2/studies?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<StudyResponse>>("/brapi/v2/studies?page=0&pageSize=10");
   return response.result.data.map((study) => ({
     value: study.studyDbId,
     label: study.studyName || study.studyDbId,
@@ -188,7 +188,7 @@ const studyContextLoader = createCachedLoader(async () => {
 
 const observationUnitContextLoader = createCachedLoader(async () => {
   const response = await request<BrapiListResponse<ObservationUnitResponse>>(
-    "/brapi/v2/observationunits?page=0&pageSize=1000",
+    "/brapi/v2/observationunits?page=0&pageSize=10",
   );
   return response.result.data.map((unit) => ({
     value: unit.observationUnitDbId,
@@ -198,12 +198,12 @@ const observationUnitContextLoader = createCachedLoader(async () => {
 });
 
 const plateRowsLoader = createCachedLoader(async () => {
-  const response = await request<BrapiListResponse<PlateRecord>>("/brapi/v2/plates?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<PlateRecord>>("/brapi/v2/plates?page=0&pageSize=10");
   return response.result.data.map(mapPlate);
 });
 
 const sampleRowsAllLoader = createCachedLoader(async () => {
-  const response = await request<BrapiListResponse<SampleRecord>>("/brapi/v2/samples?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<SampleRecord>>("/brapi/v2/samples?page=0&pageSize=10");
   return response.result.data.map(mapSample);
 });
 
@@ -238,7 +238,7 @@ function hasSampleServerFilter(query?: SampleQuery, plateDbId?: string) {
 
 async function loadRawPlates(query?: PlateQuery, force = false): Promise<PlateRecord[]> {
   if (hasPlateServerFilter(query)) {
-    const params = new URLSearchParams({ page: "0", pageSize: "1000" });
+    const params = new URLSearchParams({ page: "0", pageSize: "10" });
     if (query?.program_id && query.program_id !== NONE_SELECT_VALUE) params.set("programDbId", query.program_id);
     if (query?.trial_id && query.trial_id !== NONE_SELECT_VALUE) params.set("trialDbId", query.trial_id);
     if (query?.study_id && query.study_id !== NONE_SELECT_VALUE) params.set("studyDbId", query.study_id);
@@ -251,7 +251,7 @@ async function loadRawPlates(query?: PlateQuery, force = false): Promise<PlateRe
 
 async function loadRawSamples(query?: SampleQuery, plateDbId?: string, force = false): Promise<SampleRecord[]> {
   if (hasSampleServerFilter(query, plateDbId)) {
-    const params = new URLSearchParams({ page: "0", pageSize: "1000" });
+    const params = new URLSearchParams({ page: "0", pageSize: "10" });
     const effectivePlateId = plateDbId || optionalText(query?.plate_id);
     if (effectivePlateId) params.set("plateDbId", effectivePlateId);
     if (query?.sample_name) params.set("sampleName", query.sample_name);
@@ -382,7 +382,7 @@ function filterPlates(plates: PlateRecord[], query: PlateQuery) {
 
 const plateBody = (payload: PlatePayload) => {
   const body: Record<string, unknown> = {
-    plateName: requiredText(payload.plate_name, "请填写样本板名称"),
+    plateName: requiredText(payload.plate_name, "????????"),
   };
   const plateBarcode = optionalText(payload.plate_barcode);
   const plateFormat = optionalText(payload.plate_format);
@@ -409,7 +409,7 @@ const sampleBody = (payload: SamplePayload, plateFormat?: string | null) => {
   validatePlateWell(plateFormat ?? null, row, column, well);
 
   const body: Record<string, unknown> = {
-    sampleName: requiredText(payload.sample_name, "请填写样本名称"),
+    sampleName: requiredText(payload.sample_name, "???????"),
   };
 
   const optionalFields: Array<[string, unknown]> = [
@@ -675,15 +675,15 @@ export function normalizeSampleFormData(record: SampleRecord): Record<string, un
 export async function deleteSampleRow(id: string): Promise<void> {
   const callsetCount = await countCallsetsBySample(id);
   if (callsetCount > 0) {
-    throw new Error(`该样本已有 ${callsetCount} 个 CallSet 关联，无法删除。请先处理下游基因型数据。`);
+    throw new Error(`????? ${callsetCount} ? CallSet ????????????????????`);
   }
-  throw new Error("BrAPI Samples 接口暂不支持 DELETE，请在后端扩展删除能力后再启用");
+  throw new Error("BrAPI Samples ?????? DELETE???????????????");
 }
 
 export async function deletePlateRow(id: string): Promise<void> {
   const count = await countSamplesByPlate(id);
   if (count > 0) {
-    throw new Error(`该样本板下仍有 ${count} 个样本，请先迁移或删除样本后再操作。BrAPI 暂不支持 DELETE /plates`);
+    throw new Error(`??????? ${count} ??????????????????BrAPI ???? DELETE /plates`);
   }
-  throw new Error("BrAPI Plates 接口暂不支持 DELETE，请在后端扩展删除能力后再启用");
+  throw new Error("BrAPI Plates ?????? DELETE???????????????");
 }

frontend/src/app/(app)/genotyping/variant-set/api.ts

@@ -0,0 +1,294 @@
+import { createCachedLoader, loadStudyOptions, type SelectOption as CachedSelectOption } from "@/services/dropdownCache";
+import { getAuthToken } from "@/utils/token";
+import {
+  NONE_SELECT_VALUE,
+  type SelectOption,
+  type VariantSetDetail,
+  type VariantSetQuery,
+  type VariantSetRecord,
+} from "./types";
+
+interface BrapiPagination {
+  currentPage: number;
+  pageSize: number;
+  totalCount: number;
+  totalPages: number;
+}
+
+interface BrapiListResponse<T> {
+  metadata: {
+    pagination: BrapiPagination;
+    status: Array<Record<string, unknown>>;
+    datafiles: Array<Record<string, unknown>>;
+  };
+  result: {
+    data: T[];
+  };
+}
+
+interface BrapiSingleResponse<T> {
+  metadata: {
+    pagination: BrapiPagination;
+    status: Array<Record<string, unknown>>;
+    datafiles: Array<Record<string, unknown>>;
+  };
+  result: T;
+}
+
+interface ReferenceSetResponse {
+  referenceSetDbId: string;
+  referenceSetName: string | null;
+}
+
+interface StudyLookup {
+  studyDbId: string;
+  studyName: string | null;
+}
+
+type VariantSetPayload = Partial<Record<
+  "id" | "variant_set_name" | "reference_set_id" | "study_id",
+  unknown
+>>;
+
+const apiBase = () => {
+  if (typeof window !== "undefined") return "";
+  return process.env.API_BASE_URL || process.env.NEXT_PUBLIC_API_BASE_URL || "http://localhost:8000";
+};
+
+async function request<T>(path: string, init?: RequestInit): Promise<T> {
+  const token = getAuthToken();
+  const response = await fetch(`${apiBase()}${path}`, {
+    ...init,
+    headers: {
+      "Content-Type": "application/json",
+      ...(token ? { Authorization: `Bearer ${token}` } : {}),
+      ...(init?.headers || {}),
+    },
+  });
+
+  if (!response.ok) {
+    const detail = await response.text();
+    throw new Error(detail || `Request failed: ${response.status}`);
+  }
+  return response.json() as Promise<T>;
+}
+
+const optionalText = (value: unknown) => {
+  const normalized = String(value ?? "").trim();
+  if (!normalized || normalized === NONE_SELECT_VALUE) return null;
+  return normalized;
+};
+
+const requiredText = (value: unknown, message: string) => {
+  const normalized = optionalText(value);
+  if (!normalized) throw new Error(message);
+  return normalized;
+};
+
+const mapVariantSet = (
+  item: VariantSetRecord,
+  referenceSets: ReferenceSetResponse[],
+  studies: StudyLookup[],
+): VariantSetRecord => {
+  const referenceSetDbId = item.referenceSetDbId || item.reference_set_id || null;
+  const studyDbId = item.studyDbId || item.study_id || null;
+  const referenceSet = referenceSets.find((entry) => entry.referenceSetDbId === referenceSetDbId);
+  const study = studies.find((entry) => entry.studyDbId === studyDbId);
+
+  return {
+    ...item,
+    id: item.variantSetDbId || item.id,
+    variant_set_name: item.variant_set_name || item.variantSetName || null,
+    reference_set_id: referenceSetDbId,
+    reference_set_name: item.reference_set_name || referenceSet?.referenceSetName || null,
+    study_id: studyDbId,
+    study_name: item.study_name || study?.studyName || null,
+    variant_count: item.variant_count ?? item.variantCount ?? null,
+    callset_count: item.callset_count ?? item.callSetCount ?? null,
+    analysis_count: item.analysis_count ?? item.analysis?.length ?? null,
+    format_count: item.format_count ?? item.availableFormats?.length ?? null,
+  };
+};
+
+const variantSetBody = (payload: VariantSetPayload) => ({
+  variantSetName: requiredText(payload.variant_set_name, "VariantSet 名称不能为空"),
+  referenceSetDbId: optionalText(payload.reference_set_id),
+  studyDbId: optionalText(payload.study_id),
+});
+
+export const normalizeVariantSetFormData = (row: VariantSetRecord) => ({
+  id: row.id,
+  variant_set_name: row.variant_set_name || row.variantSetName || "",
+  reference_set_id: row.reference_set_id && row.reference_set_id !== NONE_SELECT_VALUE
+    ? row.reference_set_id
+    : NONE_SELECT_VALUE,
+  study_id: row.study_id && row.study_id !== NONE_SELECT_VALUE ? row.study_id : NONE_SELECT_VALUE,
+});
+
+const referenceSetLoader = createCachedLoader(async () => {
+  const response = await request<BrapiListResponse<ReferenceSetResponse>>("/brapi/v2/referencesets?page=0&pageSize=10");
+  return response.result.data;
+});
+
+const variantSetListLoader = createCachedLoader(async () => {
+  const response = await request<BrapiListResponse<VariantSetRecord>>("/brapi/v2/variantsets?page=0&pageSize=10");
+  return response.result.data;
+});
+
+const toStudyLookup = (studies: CachedSelectOption[]): StudyLookup[] =>
+  studies.map((item) => ({ studyDbId: item.value, studyName: item.label }));
+
+const filterVariantSetRows = (
+  rows: VariantSetRecord[],
+  query: VariantSetQuery | undefined,
+  referenceSets: ReferenceSetResponse[],
+  studies: StudyLookup[],
+): VariantSetRecord[] => {
+  const nameFilter = String(query?.variant_set_name ?? "").trim().toLowerCase();
+  const referenceSetId = optionalText(query?.reference_set_id);
+  const studyId = optionalText(query?.study_id);
+
+  return rows
+    .map((item) => mapVariantSet(item, referenceSets, studies))
+    .filter((item) => {
+      if (nameFilter && !String(item.variant_set_name ?? "").toLowerCase().includes(nameFilter)) return false;
+      if (referenceSetId && item.reference_set_id !== referenceSetId) return false;
+      if (studyId && item.study_id !== studyId) return false;
+      return true;
+    });
+};
+
+export function invalidateVariantSetPageCache() {
+  referenceSetLoader.invalidate();
+  variantSetListLoader.invalidate();
+}
+
+export async function fetchVariantSetOptions(force = false): Promise<{
+  referenceSets: SelectOption[];
+  studies: SelectOption[];
+}> {
+  const [referenceSets, studies] = await Promise.all([
+    referenceSetLoader.load(force),
+    loadStudyOptions(force),
+  ]);
+
+  return {
+    referenceSets: referenceSets.map((item) => ({
+      value: item.referenceSetDbId,
+      label: item.referenceSetName || item.referenceSetDbId,
+    })),
+    studies,
+  };
+}
+
+export async function fetchVariantSetRows(query?: VariantSetQuery, force = false): Promise<VariantSetRecord[]> {
+  const [referenceSets, studies, variantSets] = await Promise.all([
+    referenceSetLoader.load(force),
+    loadStudyOptions(force),
+    variantSetListLoader.load(force),
+  ]);
+  return filterVariantSetRows(variantSets, query, referenceSets, toStudyLookup(studies));
+}
+
+export async function fetchVariantSetDetail(variantSetDbId: string): Promise<VariantSetDetail> {
+  const [detail, options] = await Promise.all([
+    request<BrapiSingleResponse<VariantSetDetail>>(`/brapi/v2/variantsets/${encodeURIComponent(variantSetDbId)}`),
+    fetchVariantSetOptions(),
+  ]);
+
+  const referenceSet = options.referenceSets.find((item) => item.value === detail.result.referenceSetDbId);
+  const study = options.studies.find((item) => item.value === detail.result.studyDbId);
+
+  return {
+    ...mapVariantSet(detail.result, [], []),
+    id: detail.result.variantSetDbId || variantSetDbId,
+    variant_set_name: detail.result.variantSetName || detail.result.variant_set_name || null,
+    reference_set_id: detail.result.referenceSetDbId || null,
+    reference_set_name: referenceSet?.label || null,
+    study_id: detail.result.studyDbId || null,
+    study_name: study?.label || null,
+    variant_count: detail.result.variantCount ?? null,
+    callset_count: detail.result.callSetCount ?? null,
+    analysis: detail.result.analysis || [],
+    availableFormats: detail.result.availableFormats || [],
+    analysis_count: detail.result.analysis?.length ?? 0,
+    format_count: detail.result.availableFormats?.length ?? 0,
+  };
+}
+
+export async function fetchVariantSetVariants(variantSetDbId: string) {
+  const response = await request<BrapiListResponse<Record<string, unknown>>>(
+    `/brapi/v2/variantsets/${encodeURIComponent(variantSetDbId)}/variants?pageSize=10`,
+  );
+  return response.result.data;
+}
+
+export async function fetchVariantSetCallsets(variantSetDbId: string) {
+  const response = await request<BrapiListResponse<Record<string, unknown>>>(
+    `/brapi/v2/variantsets/${encodeURIComponent(variantSetDbId)}/callsets?page=0&pageSize=10`,
+  );
+  return response.result.data;
+}
+
+export async function createVariantSetRow(payload: VariantSetPayload): Promise<VariantSetRecord> {
+  const response = await request<BrapiListResponse<VariantSetRecord>>("/brapi/v2/variantsets", {
+    method: "POST",
+    body: JSON.stringify({
+      variantSetDbId: requiredText(payload.id, "VariantSet ID 不能为空"),
+      ...variantSetBody(payload),
+    }),
+  });
+  invalidateVariantSetPageCache();
+  const [referenceSets, studies] = await Promise.all([
+    referenceSetLoader.load(true),
+    loadStudyOptions(true),
+  ]);
+  return mapVariantSet(response.result.data[0], referenceSets, toStudyLookup(studies));
+}
+
+export async function updateVariantSetRow(id: string, payload: VariantSetPayload): Promise<VariantSetRecord> {
+  const requestedId = optionalText(payload.id);
+  if (requestedId && requestedId !== id) {
+    throw new Error("VariantSet ID 不可修改，请新建记录");
+  }
+  const response = await request<BrapiSingleResponse<VariantSetRecord>>(
+    `/brapi/v2/variantsets/${encodeURIComponent(id)}`,
+    {
+      method: "PUT",
+      body: JSON.stringify(variantSetBody(payload)),
+    },
+  );
+  invalidateVariantSetPageCache();
+  const [referenceSets, studies] = await Promise.all([
+    referenceSetLoader.load(true),
+    loadStudyOptions(true),
+  ]);
+  return mapVariantSet(response.result, referenceSets, toStudyLookup(studies));
+}
+
+export async function deleteVariantSetRow(id: string): Promise<void> {
+  await request<BrapiSingleResponse<VariantSetRecord>>(`/brapi/v2/variantsets/${encodeURIComponent(id)}`, {
+    method: "DELETE",
+  });
+  invalidateVariantSetPageCache();
+}
+
+export async function loadVariantSetPageData(options?: { query?: VariantSetQuery; force?: boolean }) {
+  const force = options?.force ?? false;
+  const [referenceSets, studies, variantSets] = await Promise.all([
+    referenceSetLoader.load(force),
+    loadStudyOptions(force),
+    variantSetListLoader.load(force),
+  ]);
+
+  return {
+    options: {
+      referenceSets: referenceSets.map((item) => ({
+        value: item.referenceSetDbId,
+        label: item.referenceSetName || item.referenceSetDbId,
+      })),
+      studies,
+    },
+    rows: filterVariantSetRows(variantSets, options?.query, referenceSets, toStudyLookup(studies)),
+  };
+}

frontend/src/app/(app)/genotyping/variant-set/components/VariantSetTab.tsx

@@ -0,0 +1,199 @@
+"use client";
+
+import Link from "next/link";
+import { useCallback, useMemo, useState } from "react";
+import { Layers, RotateCcw, Search } from "lucide-react";
+import { BrapiEntityPage, type BrapiFormField } from "@/components/brapi/BrapiEntityPage";
+import { Badge } from "@/components/ui/badge";
+import { Button } from "@/components/ui/button";
+import { Input } from "@/components/ui/input";
+import { Label } from "@/components/ui/label";
+import { Select, SelectContent, SelectItem, SelectTrigger, SelectValue } from "@/components/ui/select";
+import {
+  createVariantSetRow,
+  deleteVariantSetRow,
+  fetchVariantSetDetail,
+  loadVariantSetPageData,
+  normalizeVariantSetFormData,
+  updateVariantSetRow,
+} from "../api";
+import { NONE_SELECT_VALUE, type SelectOption, type VariantSetQuery } from "../types";
+
+const emptyQuery = (): VariantSetQuery => ({
+  variant_set_name: "",
+  reference_set_id: NONE_SELECT_VALUE,
+  study_id: NONE_SELECT_VALUE,
+});
+
+const optionOrNone = (label: string, options: SelectOption[]) => [
+  { value: NONE_SELECT_VALUE, label },
+  ...options,
+];
+
+export function VariantSetTab() {
+  const [referenceSetOptions, setReferenceSetOptions] = useState<SelectOption[]>([]);
+  const [studyOptions, setStudyOptions] = useState<SelectOption[]>([]);
+  const [draftQuery, setDraftQuery] = useState<VariantSetQuery>(emptyQuery);
+  const [appliedQuery, setAppliedQuery] = useState<VariantSetQuery>(emptyQuery);
+
+  const loadRows = useCallback(async () => {
+    const { options, rows } = await loadVariantSetPageData({ query: appliedQuery });
+    setReferenceSetOptions(options.referenceSets);
+    setStudyOptions(options.studies);
+    return rows as unknown as Record<string, unknown>[];
+  }, [appliedQuery]);
+
+  const fetchRecord = useCallback(async (id: string) => {
+    const detail = await fetchVariantSetDetail(id);
+    return normalizeVariantSetFormData(detail);
+  }, []);
+
+  const fields = useMemo<BrapiFormField[]>(() => [
+    { key: "id", label: "VariantSet ID", type: "text", required: true, placeholder: "variantset-001" },
+    {
+      key: "variant_set_name",
+      label: "变异集合名称",
+      type: "text",
+      required: true,
+      placeholder: "如 Hapmap 2026",
+    },
+    {
+      key: "reference_set_id",
+      label: "ReferenceSet",
+      type: "select",
+      options: optionOrNone("不关联 ReferenceSet", referenceSetOptions),
+    },
+    {
+      key: "study_id",
+      label: "Study",
+      type: "select",
+      options: optionOrNone("不关联 Study", studyOptions),
+    },
+  ], [referenceSetOptions, studyOptions]);
+
+  const renderFormExtra = useCallback(() => (
+    <div className="col-span-2 rounded-lg border border-violet-100 bg-violet-50/60 p-3 text-xs text-violet-900 dark:border-violet-900/40 dark:bg-violet-950/30 dark:text-violet-100">
+      <p className="font-medium">ReferenceSet 一致性</p>
+      <p className="mt-1 text-violet-800/80 dark:text-violet-200/80">
+        建议为 VariantSet 指定 ReferenceSet；下属 Variant 的 reference_set_id 应与此处保持一致。
+      </p>
+    </div>
+  ), []);
+
+  const renderQueryForm = useCallback(() => (
+    <div className="rounded-xl border border-slate-200 bg-white p-4 dark:border-slate-800 dark:bg-slate-950">
+      <div className="grid gap-3 md:grid-cols-2 xl:grid-cols-4">
+        <div className="space-y-1.5">
+          <Label className="text-xs text-slate-500">变异集合名称</Label>
+          <Input
+            value={draftQuery.variant_set_name ?? ""}
+            onChange={(event) => setDraftQuery((current) => ({ ...current, variant_set_name: event.target.value }))}
+            placeholder="variantSetName 模糊匹配"
+          />
+        </div>
+        <div className="space-y-1.5">
+          <Label className="text-xs text-slate-500">ReferenceSet</Label>
+          <Select
+            value={draftQuery.reference_set_id ?? NONE_SELECT_VALUE}
+            onValueChange={(value) => setDraftQuery((current) => ({ ...current, reference_set_id: value }))}
+          >
+            <SelectTrigger><SelectValue placeholder="全部" /></SelectTrigger>
+            <SelectContent>
+              <SelectItem value={NONE_SELECT_VALUE}>全部</SelectItem>
+              {referenceSetOptions.map((option) => (
+                <SelectItem key={option.value} value={option.value}>{option.label}</SelectItem>
+              ))}
+            </SelectContent>
+          </Select>
+        </div>
+        <div className="space-y-1.5">
+          <Label className="text-xs text-slate-500">Study</Label>
+          <Select
+            value={draftQuery.study_id ?? NONE_SELECT_VALUE}
+            onValueChange={(value) => setDraftQuery((current) => ({ ...current, study_id: value }))}
+          >
+            <SelectTrigger><SelectValue placeholder="全部" /></SelectTrigger>
+            <SelectContent>
+              <SelectItem value={NONE_SELECT_VALUE}>全部</SelectItem>
+              {studyOptions.map((option) => (
+                <SelectItem key={option.value} value={option.value}>{option.label}</SelectItem>
+              ))}
+            </SelectContent>
+          </Select>
+        </div>
+      </div>
+      <div className="mt-3 flex flex-wrap gap-2">
+        <Button type="button" variant="outline" className="gap-2" onClick={() => {
+          const reset = emptyQuery();
+          setDraftQuery(reset);
+          setAppliedQuery(reset);
+        }}>
+          <RotateCcw className="h-4 w-4" />
+          重置
+        </Button>
+        <Button type="button" className="gap-2" onClick={() => setAppliedQuery({ ...draftQuery })}>
+          <Search className="h-4 w-4" />
+          查询
+        </Button>
+      </div>
+    </div>
+  ), [draftQuery, referenceSetOptions, studyOptions]);
+
+  return (
+    <BrapiEntityPage
+      useEnhancedDialog
+      icon={Layers}
+      iconBg="bg-gradient-to-br from-violet-500 to-purple-600"
+      title="VariantSet 变异集合"
+      description="维护测序、芯片或 Study 下的变异位点集合，并关联 ReferenceSet 与 Study。"
+      addLabel="新增 VariantSet"
+      columns={[
+        {
+          key: "variant_set_name",
+          label: "名称",
+          render: (value, row) => {
+            const id = String(row.id ?? row.variantSetDbId ?? "");
+            const name = String(value ?? "—");
+            if (!id) return name;
+            return (
+              <Link
+                href={`/genotyping/variant-set/variant-sets/${encodeURIComponent(id)}`}
+                className="font-medium text-violet-600 hover:underline dark:text-violet-400"
+              >
+                {name}
+              </Link>
+            );
+          },
+        },
+        { key: "reference_set_name", label: "ReferenceSet" },
+        { key: "study_name", label: "Study" },
+        {
+          key: "variant_count",
+          label: "Variant 数",
+          render: (value) => <Badge variant="outline">{Number(value ?? 0)}</Badge>,
+        },
+        {
+          key: "callset_count",
+          label: "CallSet 数",
+          render: (value) => <Badge variant="outline">{Number(value ?? 0)}</Badge>,
+        },
+        { key: "analysis_count", label: "Analysis 数" },
+        { key: "format_count", label: "Formats 数" },
+      ]}
+      fields={fields}
+      data={[]}
+      stats={[{
+        label: "/brapi/v2/variantsets",
+        value: "BrAPI",
+        className: "bg-violet-50 text-violet-700 dark:bg-violet-400/10 dark:text-violet-200",
+      }]}
+      loadData={loadRows}
+      fetchRecord={fetchRecord}
+      createRecord={(payload) => createVariantSetRow(payload) as unknown as Promise<Record<string, unknown>>}
+      updateRecord={(id, payload) => updateVariantSetRow(id, payload) as unknown as Promise<Record<string, unknown>>}
+      deleteRecord={deleteVariantSetRow}
+      renderQueryForm={renderQueryForm}
+      renderFormExtra={renderFormExtra}
+    />
+  );
+}

frontend/src/app/(app)/genotyping/variant-set/page.tsx

@@ -0,0 +1,11 @@
+"use client";
+
+import { VariantSetTab } from "./components/VariantSetTab";
+
+export default function VariantSetPage() {
+  return (
+    <div className="flex min-h-full flex-col gap-4">
+      <VariantSetTab />
+    </div>
+  );
+}

frontend/src/app/(app)/genotyping/variant-set/types.ts

@@ -0,0 +1,51 @@
+export const NONE_SELECT_VALUE = "__none__";
+
+export interface SelectOption {
+  value: string;
+  label: string;
+}
+
+export interface VariantSetQuery {
+  variant_set_name?: string;
+  reference_set_id?: string;
+  study_id?: string;
+}
+
+export interface VariantSetAnalysisItem {
+  analysisDbId?: string;
+  analysisName?: string | null;
+  type?: string | null;
+  software?: string | null;
+}
+
+export interface VariantSetFormatItem {
+  dataFormat?: string | null;
+  fileFormat?: string | null;
+  fileURL?: string | null;
+}
+
+export interface VariantSetRecord {
+  id: string;
+  variantSetDbId: string;
+  variantSetName: string | null;
+  variant_set_name: string | null;
+  referenceSetDbId: string | null;
+  reference_set_id: string | null;
+  reference_set_name: string | null;
+  studyDbId: string | null;
+  study_id: string | null;
+  study_name: string | null;
+  variantCount: number | null;
+  variant_count: number | null;
+  callSetCount: number | null;
+  callset_count: number | null;
+  analysis_count: number | null;
+  format_count: number | null;
+  analysis?: VariantSetAnalysisItem[];
+  availableFormats?: VariantSetFormatItem[];
+}
+
+export interface VariantSetDetail extends VariantSetRecord {
+  analysis: VariantSetAnalysisItem[];
+  availableFormats: VariantSetFormatItem[];
+}

frontend/src/app/(app)/genotyping/variant-set/variant-sets/[variantSetDbId]/page.tsx

@@ -0,0 +1,233 @@
+"use client";
+
+import Link from "next/link";
+import { useCallback, useEffect, useState } from "react";
+import { useParams } from "next/navigation";
+import { ArrowLeft, Binary, Layers, Sigma } from "lucide-react";
+import { Badge } from "@/components/ui/badge";
+import { Button } from "@/components/ui/button";
+import { Card, CardContent, CardHeader, CardTitle } from "@/components/ui/card";
+import { Skeleton } from "@/components/ui/skeleton";
+import { Table, TableBody, TableCell, TableHead, TableHeader, TableRow } from "@/components/ui/table";
+import {
+  fetchVariantSetCallsets,
+  fetchVariantSetDetail,
+  fetchVariantSetVariants,
+} from "../../api";
+
+export default function VariantSetDetailPage() {
+  const params = useParams<{ variantSetDbId: string }>();
+  const variantSetDbId = decodeURIComponent(params.variantSetDbId);
+
+  const [loading, setLoading] = useState(true);
+  const [error, setError] = useState<string | null>(null);
+  const [detail, setDetail] = useState<Awaited<ReturnType<typeof fetchVariantSetDetail>> | null>(null);
+  const [variants, setVariants] = useState<Array<Record<string, unknown>>>([]);
+  const [callsets, setCallsets] = useState<Array<Record<string, unknown>>>([]);
+
+  const loadDetail = useCallback(async () => {
+    const [variantSet, variantRows, callsetRows] = await Promise.all([
+      fetchVariantSetDetail(variantSetDbId),
+      fetchVariantSetVariants(variantSetDbId),
+      fetchVariantSetCallsets(variantSetDbId),
+    ]);
+    setDetail(variantSet);
+    setVariants(variantRows);
+    setCallsets(callsetRows);
+  }, [variantSetDbId]);
+
+  useEffect(() => {
+    let mounted = true;
+    setLoading(true);
+    setError(null);
+    loadDetail()
+      .catch((event) => {
+        if (!mounted) return;
+        setError(event instanceof Error ? event.message : "加载 VariantSet 详情失败");
+      })
+      .finally(() => {
+        if (mounted) setLoading(false);
+      });
+    return () => { mounted = false; };
+  }, [loadDetail]);
+
+  if (loading) {
+    return (
+      <div className="space-y-4 p-1">
+        <Skeleton className="h-10 w-48" />
+        <Skeleton className="h-36 w-full" />
+        <Skeleton className="h-96 w-full" />
+      </div>
+    );
+  }
+
+  if (error || !detail) {
+    return (
+      <div className="rounded-xl border border-destructive/20 bg-destructive/10 px-4 py-6 text-sm text-destructive">
+        {error || "VariantSet 不存在"}
+        <div className="mt-4">
+          <Button asChild variant="outline">
+            <Link href="/genotyping/variant-set"><ArrowLeft className="mr-2 h-4 w-4" />返回列表</Link>
+          </Button>
+        </div>
+      </div>
+    );
+  }
+
+  const hasDependencies = (detail.variant_count ?? 0) > 0
+    || (detail.callset_count ?? 0) > 0
+    || (detail.analysis_count ?? 0) > 0
+    || (detail.format_count ?? 0) > 0;
+
+  return (
+    <div className="flex min-h-full flex-col gap-4">
+      <div className="flex flex-wrap items-center justify-between gap-3">
+        <Button asChild variant="outline" size="sm">
+          <Link href="/genotyping/variant-set"><ArrowLeft className="mr-2 h-4 w-4" />返回 VariantSet 列表</Link>
+        </Button>
+        {hasDependencies ? (
+          <Badge variant="outline" className="border-amber-200 bg-amber-50 text-amber-800 dark:border-amber-900 dark:bg-amber-950 dark:text-amber-200">
+            删除前请确认无 Variant、CallSet、Analysis 或 Format 引用
+          </Badge>
+        ) : null}
+      </div>
+
+      <Card>
+        <CardHeader className="pb-3">
+          <CardTitle className="flex items-center gap-2 text-lg">
+            <Layers className="h-5 w-5 text-violet-500" />
+            {detail.variant_set_name || detail.id}
+          </CardTitle>
+        </CardHeader>
+        <CardContent className="grid gap-3 text-sm sm:grid-cols-2 lg:grid-cols-4">
+          <div><span className="text-slate-500">VariantSet ID：</span>{detail.id}</div>
+          <div><span className="text-slate-500">ReferenceSet：</span>{detail.reference_set_name || "N/A"}</div>
+          <div><span className="text-slate-500">Study：</span>{detail.study_name || "N/A"}</div>
+          <div><span className="text-slate-500">Variant 数：</span>{detail.variant_count ?? 0}</div>
+          <div><span className="text-slate-500">CallSet 数：</span>{detail.callset_count ?? 0}</div>
+        </CardContent>
+      </Card>
+
+      <Card>
+        <CardHeader className="pb-3">
+          <CardTitle className="flex items-center gap-2 text-base">
+            <Sigma className="h-4 w-4 text-rose-500" />
+            Variants
+          </CardTitle>
+        </CardHeader>
+        <CardContent>
+          {variants.length === 0 ? (
+            <p className="text-sm text-slate-500">暂无 Variant 位点。</p>
+          ) : (
+            <Table>
+              <TableHeader>
+                <TableRow>
+                  <TableHead>Variant ID</TableHead>
+                  <TableHead>名称</TableHead>
+                  <TableHead>类型</TableHead>
+                  <TableHead>起点</TableHead>
+                  <TableHead>终点</TableHead>
+                </TableRow>
+              </TableHeader>
+              <TableBody>
+                {variants.slice(0, 20).map((row) => {
+                  const id = String(row.variantDbId ?? row.id ?? "");
+                  const names = Array.isArray(row.variantNames) ? row.variantNames.join(", ") : String(row.variantName ?? "—");
+                  return (
+                    <TableRow key={id}>
+                      <TableCell>
+                        {id ? (
+                          <Link href={`/genotyping/variant/variants/${encodeURIComponent(id)}`} className="text-rose-600 hover:underline dark:text-rose-400">
+                            {id}
+                          </Link>
+                        ) : "—"}
+                      </TableCell>
+                      <TableCell>{names}</TableCell>
+                      <TableCell>{String(row.variantType ?? "—")}</TableCell>
+                      <TableCell>{String(row.start ?? "—")}</TableCell>
+                      <TableCell>{String(row.end ?? "—")}</TableCell>
+                    </TableRow>
+                  );
+                })}
+              </TableBody>
+            </Table>
+          )}
+          {variants.length > 20 ? (
+            <p className="mt-2 text-xs text-slate-500">仅展示前 20 条，完整列表请前往 Variant 管理页筛选。</p>
+          ) : null}
+        </CardContent>
+      </Card>
+
+      <Card>
+        <CardHeader className="pb-3">
+          <CardTitle className="flex items-center gap-2 text-base">
+            <Binary className="h-4 w-4 text-sky-500" />
+            CallSets
+          </CardTitle>
+        </CardHeader>
+        <CardContent>
+          {callsets.length === 0 ? (
+            <p className="text-sm text-slate-500">暂无 CallSet。</p>
+          ) : (
+            <Table>
+              <TableHeader>
+                <TableRow>
+                  <TableHead>CallSet ID</TableHead>
+                  <TableHead>名称</TableHead>
+                  <TableHead>Sample</TableHead>
+                </TableRow>
+              </TableHeader>
+              <TableBody>
+                {callsets.map((row) => (
+                  <TableRow key={String(row.callSetDbId ?? row.id ?? Math.random())}>
+                    <TableCell>{String(row.callSetDbId ?? "—")}</TableCell>
+                    <TableCell>{String(row.callSetName ?? "—")}</TableCell>
+                    <TableCell>{String(row.sampleName ?? row.sampleDbId ?? "—")}</TableCell>
+                  </TableRow>
+                ))}
+              </TableBody>
+            </Table>
+          )}
+        </CardContent>
+      </Card>
+
+      <div className="grid gap-4 lg:grid-cols-2">
+        <Card>
+          <CardHeader className="pb-3">
+            <CardTitle className="text-base">Analysis</CardTitle>
+          </CardHeader>
+          <CardContent className="space-y-2 text-sm">
+            {(detail.analysis || []).length === 0 ? (
+              <p className="text-slate-500">暂无 Analysis。</p>
+            ) : (
+              detail.analysis.map((item) => (
+                <div key={item.analysisDbId || item.analysisName || Math.random()} className="rounded-lg border p-3 dark:border-slate-800">
+                  <div className="font-medium">{item.analysisName || item.analysisDbId}</div>
+                  <div className="mt-1 text-slate-500">{item.type || "—"} · {item.software || "—"}</div>
+                </div>
+              ))
+            )}
+          </CardContent>
+        </Card>
+
+        <Card>
+          <CardHeader className="pb-3">
+            <CardTitle className="text-base">Available Formats</CardTitle>
+          </CardHeader>
+          <CardContent className="space-y-2 text-sm">
+            {(detail.availableFormats || []).length === 0 ? (
+              <p className="text-slate-500">暂无可用格式。</p>
+            ) : (
+              detail.availableFormats.map((item) => (
+                <div key={`${item.dataFormat}-${item.fileFormat}-${item.fileURL}`} className="rounded-lg border p-3 dark:border-slate-800">
+                  <div className="font-medium">{item.fileFormat || item.dataFormat || "Format"}</div>
+                  <div className="mt-1 break-all text-slate-500">{item.fileURL || "—"}</div>
+                </div>
+              ))
+            )}
+          </CardContent>
+        </Card>
+      </div>
+    </div>
+  );
+}

frontend/src/app/(app)/genotyping/variant/api.ts

@@ -1,8 +1,10 @@
+import { createCachedLoader } from "@/services/dropdownCache";
 import { getAuthToken } from "@/utils/token";
 import {
   NONE_SELECT_VALUE,
   type CallRecord,
   type SelectOption,
+  type VariantQuery,
   type VariantRecord,
 } from "./types";
 
@@ -135,12 +137,18 @@ const genotypeToText = (value: unknown) => {
   return null;
 };
 
-const mapVariant = (variant: VariantRecord): VariantRecord => ({
+export const mapVariant = (variant: VariantRecord): VariantRecord => ({
   ...variant,
   id: variant.variantDbId || variant.variantId || variant.id,
-  variant_name: variant.variant_name || variant.variantName || null,
+  variant_name: variant.variant_name
+    || variant.variantName
+    || (Array.isArray(variant.variantNames) ? variant.variantNames[0] : null)
+    || null,
   variant_type: variant.variant_type || variant.variantType || null,
-  variant_set_id: variant.variant_set_id || variant.variantSetDbId || null,
+  variant_set_id: variant.variant_set_id
+    || variant.variantSetDbId
+    || (Array.isArray(variant.variantSetDbId) ? variant.variantSetDbId[0] : null)
+    || null,
   variant_set_name: variant.variant_set_name || variant.variantSetName || null,
   reference_set_id: variant.reference_set_id || variant.referenceSetDbId || null,
   reference_set_name: variant.reference_set_name || variant.referenceSetName || null,
@@ -188,49 +196,154 @@ const callBody = (payload: CallPayload) => ({
   phaseSet: optionalText(payload.phase_set),
 });
 
-export async function fetchVariantRows(): Promise<VariantRecord[]> {
+export const normalizeVariantFormData = (row: VariantRecord) => ({
-  const response = await request<BrapiListResponse<VariantRecord>>("/brapi/v2/variants?page=0&pageSize=1000");
+  id: row.id,
+  variant_name: row.variant_name || "",
+  variant_type: row.variant_type && row.variant_type !== NONE_SELECT_VALUE ? row.variant_type : NONE_SELECT_VALUE,
+  variant_set_id: row.variant_set_id && row.variant_set_id !== NONE_SELECT_VALUE ? row.variant_set_id : NONE_SELECT_VALUE,
+  reference_set_id: row.reference_set_id && row.reference_set_id !== NONE_SELECT_VALUE ? row.reference_set_id : NONE_SELECT_VALUE,
+  start: row.start ?? "",
+  end: row.end ?? "",
+  reference_bases: row.reference_bases || "",
+  svlen: row.svlen ?? "",
+  filters_applied: row.filters_applied === true ? "true" : row.filters_applied === false ? "false" : NONE_SELECT_VALUE,
+  filters_passed: row.filters_passed === true ? "true" : row.filters_passed === false ? "false" : NONE_SELECT_VALUE,
+});
+
+const referenceSetLoader = createCachedLoader(async () => {
+  const response = await request<BrapiListResponse<ReferenceSetResponse>>("/brapi/v2/referencesets?page=0&pageSize=10");
+  return response.result.data;
+});
+
+const variantSetLoader = createCachedLoader(async () => {
+  const response = await request<BrapiListResponse<VariantSetResponse>>("/brapi/v2/variantsets?page=0&pageSize=10");
+  return response.result.data;
+});
+
+const callSetLoader = createCachedLoader(async () => {
+  const response = await request<BrapiListResponse<CallSetResponse>>("/brapi/v2/callsets?page=0&pageSize=10");
+  return response.result.data;
+});
+
+const variantRowsLoader = createCachedLoader(async () => {
+  const response = await request<BrapiListResponse<VariantRecord>>("/brapi/v2/variants?page=0&pageSize=10");
   return response.result.data.map(mapVariant);
+});
+
+function enrichVariantRows(
+  rows: VariantRecord[],
+  referenceSets: ReferenceSetResponse[],
+  variantSets: VariantSetResponse[],
+): VariantRecord[] {
+  return rows.map((row) => {
+    const referenceSet = referenceSets.find((item) => item.referenceSetDbId === row.reference_set_id);
+    const variantSet = variantSets.find((item) => item.variantSetDbId === row.variant_set_id);
+    return {
+      ...row,
+      reference_set_name: row.reference_set_name || referenceSet?.referenceSetName || null,
+      variant_set_name: row.variant_set_name || variantSet?.variantSetName || null,
+    };
+  });
 }
 
-export async function fetchCallRows(): Promise<CallRecord[]> {
+function filterVariantRows(rows: VariantRecord[], query?: VariantQuery): VariantRecord[] {
-  const response = await request<BrapiListResponse<CallRecord>>("/brapi/v2/calls?page=0&pageSize=1000");
+  const nameFilter = String(query?.variant_name ?? "").trim().toLowerCase();
-  return response.result.data.map(mapCall);
+  const typeFilter = optionalText(query?.variant_type);
+  const variantSetId = optionalText(query?.variant_set_id);
+  const referenceSetId = optionalText(query?.reference_set_id);
+
+  return rows.filter((row) => {
+    if (nameFilter && !String(row.variant_name ?? "").toLowerCase().includes(nameFilter)) return false;
+    if (typeFilter && row.variant_type !== typeFilter) return false;
+    if (variantSetId && row.variant_set_id !== variantSetId) return false;
+    if (referenceSetId && row.reference_set_id !== referenceSetId) return false;
+    return true;
+  });
 }
 
-export async function fetchVariantOptions(): Promise<{
+function buildVariantOptions(
+  referenceSets: ReferenceSetResponse[],
+  variantSets: VariantSetResponse[],
+  callSets: CallSetResponse[],
+  variants: VariantRecord[],
+) {
+  return {
+    referenceSets: referenceSets.map((item) => ({
+      value: item.referenceSetDbId,
+      label: item.referenceSetName || item.referenceSetDbId,
+    })),
+    variantSets: variantSets.map((item) => ({
+      value: item.variantSetDbId,
+      label: `${item.variantSetName || item.variantSetDbId}${item.referenceSetDbId ? ` / ${item.referenceSetDbId}` : ""}`,
+    })),
+    callSets: callSets.map((item) => ({
+      value: item.callSetDbId,
+      label: `${item.callSetName || item.callSetDbId}${item.sampleName || item.sampleDbId ? ` / ${item.sampleName || item.sampleDbId}` : ""}`,
+    })),
+    variants: variants.map((item) => ({
+      value: item.id,
+      label: `${item.variant_name || item.id}${item.variant_type ? ` / ${item.variant_type}` : ""}`,
+    })),
+  };
+}
+
+export function invalidateVariantPageCache() {
+  referenceSetLoader.invalidate();
+  variantSetLoader.invalidate();
+  callSetLoader.invalidate();
+  variantRowsLoader.invalidate();
+}
+
+export async function fetchVariantOptions(force = false): Promise<{
   referenceSets: SelectOption[];
   variantSets: SelectOption[];
   callSets: SelectOption[];
   variants: SelectOption[];
 }> {
   const [referenceSets, variantSets, callSets, variants] = await Promise.all([
-    request<BrapiListResponse<ReferenceSetResponse>>("/brapi/v2/referencesets?page=0&pageSize=1000"),
+    referenceSetLoader.load(force),
-    request<BrapiListResponse<VariantSetResponse>>("/brapi/v2/variantsets?page=0&pageSize=1000"),
+    variantSetLoader.load(force),
-    request<BrapiListResponse<CallSetResponse>>("/brapi/v2/callsets?page=0&pageSize=1000"),
+    callSetLoader.load(force),
-    request<BrapiListResponse<VariantRecord>>("/brapi/v2/variants?page=0&pageSize=1000"),
+    variantRowsLoader.load(force),
   ]);
 
+  return buildVariantOptions(referenceSets, variantSets, callSets, variants);
+}
+
+export async function fetchVariantRows(query?: VariantQuery): Promise<VariantRecord[]> {
+  const [variants, referenceSets, variantSets] = await Promise.all([
+    variantRowsLoader.load(),
+    referenceSetLoader.load(),
+    variantSetLoader.load(),
+  ]);
+
+  return filterVariantRows(enrichVariantRows(variants, referenceSets, variantSets), query);
+}
+
+export async function fetchVariantDetail(variantDbId: string): Promise<VariantRecord> {
+  const [detail, options, callsResponse] = await Promise.all([
+    request<BrapiSingleResponse<VariantRecord>>(`/brapi/v2/variants/${encodeURIComponent(variantDbId)}`),
+    fetchVariantOptions(),
+    request<BrapiListResponse<CallRecord>>(`/brapi/v2/variants/${encodeURIComponent(variantDbId)}/calls?pageSize=10`),
+  ]);
+
+  const mapped = mapVariant(detail.result);
+  const referenceSet = options.referenceSets.find((item) => item.value === mapped.reference_set_id);
+  const variantSet = options.variantSets.find((item) => item.value === mapped.variant_set_id);
+
   return {
-    referenceSets: referenceSets.result.data.map((item) => ({
+    ...mapped,
-      value: item.referenceSetDbId,
+    reference_set_name: mapped.reference_set_name || referenceSet?.label || null,
-      label: item.referenceSetName || item.referenceSetDbId,
+    variant_set_name: mapped.variant_set_name || variantSet?.label || null,
-    })),
+    allele_call_count: callsResponse.result.data.length,
-    variantSets: variantSets.result.data.map((item) => ({
-      value: item.variantSetDbId,
-      label: `${item.variantSetName || item.variantSetDbId}${item.referenceSetDbId ? ` / ${item.referenceSetDbId}` : ""}`,
-    })),
-    callSets: callSets.result.data.map((item) => ({
-      value: item.callSetDbId,
-      label: `${item.callSetName || item.callSetDbId}${item.sampleName || item.sampleDbId ? ` / ${item.sampleName || item.sampleDbId}` : ""}`,
-    })),
-    variants: variants.result.data.map(mapVariant).map((item) => ({
-      value: item.id,
-      label: `${item.variant_name || item.id}${item.variant_type ? ` / ${item.variant_type}` : ""}`,
-    })),
   };
 }
 
+export async function fetchCallRows(): Promise<CallRecord[]> {
+  const response = await request<BrapiListResponse<CallRecord>>("/brapi/v2/calls?page=0&pageSize=10");
+  return response.result.data.map(mapCall);
+}
+
 export async function createVariantRow(payload: VariantPayload): Promise<VariantRecord> {
   const response = await request<BrapiListResponse<VariantRecord>>("/brapi/v2/variants", {
     method: "POST",
@@ -239,6 +352,7 @@ export async function createVariantRow(payload: VariantPayload): Promise<Variant
       ...variantBody(payload),
     }),
   });
+  invalidateVariantPageCache();
   return mapVariant(response.result.data[0]);
 }
 
@@ -249,6 +363,7 @@ export async function updateVariantRow(id: string, payload: VariantPayload): Pro
     method: "PUT",
     body: JSON.stringify(variantBody(payload)),
   });
+  invalidateVariantPageCache();
   return mapVariant(response.result);
 }
 
@@ -256,6 +371,7 @@ export async function deleteVariantRow(id: string): Promise<void> {
   await request<BrapiSingleResponse<VariantRecord>>(`/brapi/v2/variants/${encodeURIComponent(id)}`, {
     method: "DELETE",
   });
+  invalidateVariantPageCache();
 }
 
 export async function createCallRow(payload: CallPayload): Promise<CallRecord> {
@@ -284,3 +400,19 @@ export async function deleteCallRow(id: string): Promise<void> {
     method: "DELETE",
   });
 }
+
+export async function loadVariantPageData(options?: { query?: VariantQuery; force?: boolean }) {
+  const force = options?.force ?? false;
+  const [referenceSets, variantSets, callSets, variants] = await Promise.all([
+    referenceSetLoader.load(force),
+    variantSetLoader.load(force),
+    callSetLoader.load(force),
+    variantRowsLoader.load(force),
+  ]);
+
+  const enrichedRows = enrichVariantRows(variants, referenceSets, variantSets);
+  return {
+    options: buildVariantOptions(referenceSets, variantSets, callSets, variants),
+    rows: filterVariantRows(enrichedRows, options?.query),
+  };
+}

frontend/src/app/(app)/genotyping/variant/components/VariantTab.tsx

@@ -0,0 +1,241 @@
+"use client";
+
+import Link from "next/link";
+import { useCallback, useMemo, useState } from "react";
+import { useSearchParams } from "next/navigation";
+import { RotateCcw, Search, Sigma } from "lucide-react";
+import { BrapiEntityPage, type BrapiFormField } from "@/components/brapi/BrapiEntityPage";
+import { Button } from "@/components/ui/button";
+import { Input } from "@/components/ui/input";
+import { Label } from "@/components/ui/label";
+import { Select, SelectContent, SelectItem, SelectTrigger, SelectValue } from "@/components/ui/select";
+import {
+  createVariantRow,
+  deleteVariantRow,
+  fetchVariantDetail,
+  loadVariantPageData,
+  normalizeVariantFormData,
+  updateVariantRow,
+} from "../api";
+import { NONE_SELECT_VALUE, type SelectOption, type VariantQuery } from "../types";
+
+const variantTypeOptions: SelectOption[] = [
+  { value: NONE_SELECT_VALUE, label: "不指定类型" },
+  { value: "SNP", label: "SNP / 单核苷酸变异" },
+  { value: "INDEL", label: "INDEL / 插入缺失" },
+  { value: "SV", label: "SV / 结构变异" },
+  { value: "CNV", label: "CNV / 拷贝数变异" },
+];
+
+const booleanOptions: SelectOption[] = [
+  { value: NONE_SELECT_VALUE, label: "不指定" },
+  { value: "true", label: "是" },
+  { value: "false", label: "否" },
+];
+
+const emptyQuery = (): VariantQuery => ({
+  variant_name: "",
+  variant_type: NONE_SELECT_VALUE,
+  variant_set_id: NONE_SELECT_VALUE,
+  reference_set_id: NONE_SELECT_VALUE,
+});
+
+const optionOrNone = (label: string, options: SelectOption[]) => [
+  { value: NONE_SELECT_VALUE, label },
+  ...options,
+];
+
+const optionLabel = (options: SelectOption[], value: unknown) => {
+  const text = String(value ?? "").trim();
+  return options.find((option) => option.value === text)?.label || text || "N/A";
+};
+
+const boolLabel = (value: unknown) => {
+  if (value === true) return "是";
+  if (value === false) return "否";
+  return "N/A";
+};
+
+function toSelectValue(value: string | null | undefined) {
+  return value && value !== NONE_SELECT_VALUE ? value : NONE_SELECT_VALUE;
+}
+
+export function VariantTab() {
+  const searchParams = useSearchParams();
+  const [referenceSetOptions, setReferenceSetOptions] = useState<SelectOption[]>([]);
+  const [variantSetOptions, setVariantSetOptions] = useState<SelectOption[]>([]);
+  const [draftQuery, setDraftQuery] = useState<VariantQuery>(() => ({
+    ...emptyQuery(),
+    variant_set_id: toSelectValue(searchParams.get("variantSetDbId")),
+  }));
+  const [appliedQuery, setAppliedQuery] = useState<VariantQuery>(() => ({
+    ...emptyQuery(),
+    variant_set_id: toSelectValue(searchParams.get("variantSetDbId")),
+  }));
+
+  const loadRows = useCallback(async () => {
+    const { options, rows } = await loadVariantPageData({ query: appliedQuery });
+    setReferenceSetOptions(options.referenceSets);
+    setVariantSetOptions(options.variantSets);
+    return rows as unknown as Record<string, unknown>[];
+  }, [appliedQuery]);
+
+  const fetchRecord = useCallback(async (id: string) => {
+    const detail = await fetchVariantDetail(id);
+    return normalizeVariantFormData(detail);
+  }, []);
+
+  const fields = useMemo<BrapiFormField[]>(() => [
+    { key: "id", label: "Variant ID", type: "text", required: true, placeholder: "variant-001" },
+    { key: "variant_name", label: "变异名称", type: "text", required: true, placeholder: "S1_12345_A_T" },
+    { key: "variant_type", label: "变异类型", type: "select", options: variantTypeOptions },
+    {
+      key: "variant_set_id",
+      label: "VariantSet",
+      type: "select",
+      options: optionOrNone("不关联 VariantSet", variantSetOptions),
+    },
+    {
+      key: "reference_set_id",
+      label: "ReferenceSet",
+      type: "select",
+      options: optionOrNone("不关联 ReferenceSet", referenceSetOptions),
+    },
+    { key: "start", label: "起点", type: "number", placeholder: "1000" },
+    { key: "end", label: "终点", type: "number", placeholder: "1001" },
+    { key: "reference_bases", label: "参考碱基", type: "text", placeholder: "A" },
+    { key: "svlen", label: "SV 长度", type: "number", placeholder: "1" },
+    { key: "filters_applied", label: "已应用过滤", type: "select", options: booleanOptions },
+    { key: "filters_passed", label: "通过过滤", type: "select", options: booleanOptions },
+  ], [referenceSetOptions, variantSetOptions]);
+
+  const renderFormExtra = useCallback(() => (
+    <div className="col-span-2 rounded-lg border border-rose-100 bg-rose-50/60 p-3 text-xs text-rose-900 dark:border-rose-900/40 dark:bg-rose-950/30 dark:text-rose-100">
+      <p className="font-medium">位点定义说明</p>
+      <p className="mt-1 text-rose-800/80 dark:text-rose-200/80">
+        Variant 仅描述位点坐标与参考碱基，样本 genotype 结果写入 allele_call。大批量位点建议通过文件导入。
+      </p>
+    </div>
+  ), []);
+
+  const renderQueryForm = useCallback(() => (
+    <div className="rounded-xl border border-slate-200 bg-white p-4 dark:border-slate-800 dark:bg-slate-950">
+      <div className="grid gap-3 md:grid-cols-2 xl:grid-cols-5">
+        <div className="space-y-1.5">
+          <Label className="text-xs text-slate-500">变异名称</Label>
+          <Input
+            value={draftQuery.variant_name ?? ""}
+            onChange={(event) => setDraftQuery((current) => ({ ...current, variant_name: event.target.value }))}
+            placeholder="variantName 模糊匹配"
+          />
+        </div>
+        <div className="space-y-1.5">
+          <Label className="text-xs text-slate-500">变异类型</Label>
+          <Select
+            value={draftQuery.variant_type ?? NONE_SELECT_VALUE}
+            onValueChange={(value) => setDraftQuery((current) => ({ ...current, variant_type: value }))}
+          >
+            <SelectTrigger><SelectValue placeholder="全部" /></SelectTrigger>
+            <SelectContent>
+              <SelectItem value={NONE_SELECT_VALUE}>全部</SelectItem>
+              {variantTypeOptions.filter((item) => item.value !== NONE_SELECT_VALUE).map((option) => (
+                <SelectItem key={option.value} value={option.value}>{option.label}</SelectItem>
+              ))}
+            </SelectContent>
+          </Select>
+        </div>
+        <div className="space-y-1.5">
+          <Label className="text-xs text-slate-500">VariantSet</Label>
+          <Select
+            value={draftQuery.variant_set_id ?? NONE_SELECT_VALUE}
+            onValueChange={(value) => setDraftQuery((current) => ({ ...current, variant_set_id: value }))}
+          >
+            <SelectTrigger><SelectValue placeholder="全部" /></SelectTrigger>
+            <SelectContent>
+              <SelectItem value={NONE_SELECT_VALUE}>全部</SelectItem>
+              {variantSetOptions.map((option) => (
+                <SelectItem key={option.value} value={option.value}>{option.label}</SelectItem>
+              ))}
+            </SelectContent>
+          </Select>
+        </div>
+        <div className="space-y-1.5">
+          <Label className="text-xs text-slate-500">ReferenceSet</Label>
+          <Select
+            value={draftQuery.reference_set_id ?? NONE_SELECT_VALUE}
+            onValueChange={(value) => setDraftQuery((current) => ({ ...current, reference_set_id: value }))}
+          >
+            <SelectTrigger><SelectValue placeholder="全部" /></SelectTrigger>
+            <SelectContent>
+              <SelectItem value={NONE_SELECT_VALUE}>全部</SelectItem>
+              {referenceSetOptions.map((option) => (
+                <SelectItem key={option.value} value={option.value}>{option.label}</SelectItem>
+              ))}
+            </SelectContent>
+          </Select>
+        </div>
+      </div>
+      <div className="mt-3 flex flex-wrap gap-2">
+        <Button type="button" variant="outline" className="gap-2" onClick={() => {
+          const reset = emptyQuery();
+          setDraftQuery(reset);
+          setAppliedQuery(reset);
+        }}>
+          <RotateCcw className="h-4 w-4" />
+          重置
+        </Button>
+        <Button type="button" className="gap-2" onClick={() => setAppliedQuery({ ...draftQuery })}>
+          <Search className="h-4 w-4" />
+          查询
+        </Button>
+      </div>
+    </div>
+  ), [draftQuery, referenceSetOptions, variantSetOptions]);
+
+  return (
+    <BrapiEntityPage
+      useEnhancedDialog
+      icon={Sigma}
+      iconBg="bg-gradient-to-br from-rose-600 to-pink-700"
+      title="Variant 变异位点"
+      description="维护变异集合中的 SNP、INDEL、SV 等位点和坐标信息。"
+      addLabel="新增 Variant"
+      columns={[
+        {
+          key: "variant_name",
+          label: "变异名称",
+          render: (value, row) => {
+            const id = String(row.id ?? row.variantDbId ?? "");
+            const name = String(value ?? "—");
+            if (!id) return name;
+            return (
+              <Link
+                href={`/genotyping/variant/variants/${encodeURIComponent(id)}`}
+                className="font-medium text-rose-600 hover:underline dark:text-rose-400"
+              >
+                {name}
+              </Link>
+            );
+          },
+        },
+        { key: "variant_type", label: "类型", render: (value) => optionLabel(variantTypeOptions, value) },
+        { key: "variant_set_name", label: "VariantSet" },
+        { key: "reference_set_name", label: "ReferenceSet" },
+        { key: "start", label: "起点" },
+        { key: "end", label: "终点" },
+        { key: "reference_bases", label: "参考碱基" },
+        { key: "filters_passed", label: "过滤", render: boolLabel },
+      ]}
+      fields={fields}
+      data={[]}
+      stats={[{ label: "/brapi/v2/variants", value: "BrAPI", className: "bg-rose-50 text-rose-700 dark:bg-rose-400/10 dark:text-rose-200" }]}
+      loadData={loadRows}
+      fetchRecord={fetchRecord}
+      createRecord={(payload) => createVariantRow(payload) as unknown as Promise<Record<string, unknown>>}
+      updateRecord={(id, payload) => updateVariantRow(id, payload) as unknown as Promise<Record<string, unknown>>}
+      deleteRecord={deleteVariantRow}
+      renderQueryForm={() => renderQueryForm()}
+      renderFormExtra={renderFormExtra}
+    />
+  );
+}

frontend/src/app/(app)/genotyping/variant/page.tsx

@@ -1,106 +1,41 @@
-/**
- * filekorolheader: Variant / Call - 变异数据管理页面
- * 功能：Variant 变异位点维护、Call 基因型判读维护
- * 路径：/genotyping/variant
- * 规范：遵循开发项目规范.md，使用 shadcn 语义化样式和 BrAPI 数据接口
- */
 "use client";
 
-import { useCallback, useMemo, useState } from "react";
+import { Suspense, useCallback, useMemo, useState } from "react";
 import { Binary, Sigma } from "lucide-react";
 import { BrapiEntityPage, type BrapiFormField } from "@/components/brapi/BrapiEntityPage";
 import { Tabs, TabsContent, TabsList, TabsTrigger } from "@/components/ui/tabs";
+import { Skeleton } from "@/components/ui/skeleton";
+import { VariantTab } from "./components/VariantTab";
 import {
   createCallRow,
-  createVariantRow,
   deleteCallRow,
-  deleteVariantRow,
   fetchCallRows,
   fetchVariantOptions,
-  fetchVariantRows,
   updateCallRow,
-  updateVariantRow,
 } from "./api";
 import { NONE_SELECT_VALUE, type SelectOption } from "./types";
 
-const variantTypeOptions: SelectOption[] = [
+function VariantTabFallback() {
-  { value: NONE_SELECT_VALUE, label: "不指定类型" },
+  return <Skeleton className="h-96 w-full rounded-xl" />;
-  { value: "SNP", label: "SNP / 单核苷酸变异" },
+}
-  { value: "INDEL", label: "INDEL / 插入缺失" },
-  { value: "SV", label: "SV / 结构变异" },
-  { value: "CNV", label: "CNV / 拷贝数变异" },
-];
-
-const booleanOptions: SelectOption[] = [
-  { value: NONE_SELECT_VALUE, label: "不指定" },
-  { value: "true", label: "是" },
-  { value: "false", label: "否" },
-];
-
-const optionOrNone = (label: string, options: SelectOption[]) => [
-  { value: NONE_SELECT_VALUE, label },
-  ...options,
-];
-
-const optionLabel = (options: SelectOption[], value: unknown) => {
-  const text = String(value ?? "").trim();
-  return options.find((option) => option.value === text)?.label || text || "N/A";
-};
-
-const boolLabel = (value: unknown) => {
-  if (value === true) return "是";
-  if (value === false) return "否";
-  return "N/A";
-};
 
 export default function VariantPage() {
-  const [referenceSetOptions, setReferenceSetOptions] = useState<SelectOption[]>([]);
+  const [tab, setTab] = useState("variants");
-  const [variantSetOptions, setVariantSetOptions] = useState<SelectOption[]>([]);
   const [callSetOptions, setCallSetOptions] = useState<SelectOption[]>([]);
   const [variantOptions, setVariantOptions] = useState<SelectOption[]>([]);
 
   const loadOptions = useCallback(async () => {
     const options = await fetchVariantOptions();
-    setReferenceSetOptions(options.referenceSets);
-    setVariantSetOptions(options.variantSets);
     setCallSetOptions(options.callSets);
     setVariantOptions(options.variants);
+    return options;
   }, []);
 
-  const loadVariants = useCallback(async () => {
-    const [, rows] = await Promise.all([loadOptions(), fetchVariantRows()]);
-    return rows as unknown as Record<string, unknown>[];
-  }, [loadOptions]);
-
   const loadCalls = useCallback(async () => {
     const [, rows] = await Promise.all([loadOptions(), fetchCallRows()]);
     return rows as unknown as Record<string, unknown>[];
   }, [loadOptions]);
 
-  const variantFields = useMemo<BrapiFormField[]>(() => [
-    { key: "id", label: "Variant ID", type: "text", required: true, placeholder: "variant-001" },
-    { key: "variant_name", label: "变异名称", type: "text", required: true, placeholder: "S1_12345_A_T" },
-    { key: "variant_type", label: "变异类型", type: "select", options: variantTypeOptions },
-    {
-      key: "variant_set_id",
-      label: "VariantSet",
-      type: "select",
-      options: optionOrNone("不关联 VariantSet", variantSetOptions),
-    },
-    {
-      key: "reference_set_id",
-      label: "ReferenceSet",
-      type: "select",
-      options: optionOrNone("不关联 ReferenceSet", referenceSetOptions),
-    },
-    { key: "start", label: "起点", type: "number", placeholder: "1000" },
-    { key: "end", label: "终点", type: "number", placeholder: "1001" },
-    { key: "reference_bases", label: "参考碱基", type: "text", placeholder: "A" },
-    { key: "svlen", label: "SV 长度", type: "number", placeholder: "1" },
-    { key: "filters_applied", label: "已应用过滤", type: "select", options: booleanOptions },
-    { key: "filters_passed", label: "通过过滤", type: "select", options: booleanOptions },
-  ], [referenceSetOptions, variantSetOptions]);
-
   const callFields = useMemo<BrapiFormField[]>(() => [
     { key: "id", label: "Call ID", type: "text", required: true, placeholder: "call-001" },
     {
@@ -124,67 +59,48 @@ export default function VariantPage() {
   ], [callSetOptions, variantOptions]);
 
   return (
-    <Tabs defaultValue="variants" className="flex min-h-full flex-col gap-4">
+    <Tabs value={tab} onValueChange={setTab} className="flex min-h-full flex-col gap-4">
       <TabsList className="w-full justify-start overflow-x-auto rounded-lg border bg-white p-1 dark:border-slate-800 dark:bg-slate-950 sm:w-fit">
         <TabsTrigger value="variants" className="gap-2"><Sigma className="h-4 w-4" />Variants</TabsTrigger>
         <TabsTrigger value="calls" className="gap-2"><Binary className="h-4 w-4" />Calls</TabsTrigger>
       </TabsList>
 
-      <TabsContent value="variants" className="mt-0 min-h-0 flex-1">
+      {tab === "variants" ? (
-        <BrapiEntityPage
+        <TabsContent value="variants" className="mt-0 min-h-0 flex-1">
-          useEnhancedDialog
+          <Suspense fallback={<VariantTabFallback />}>
-          icon={Sigma}
+            <VariantTab />
-          iconBg="bg-gradient-to-br from-rose-600 to-pink-700"
+          </Suspense>
-          title="Variant 变异位点"
+        </TabsContent>
-          description="维护变异集合中的 SNP、INDEL、SV 等位点和坐标信息。"
+      ) : null}
-          addLabel="新增 Variant"
-          columns={[
-            { key: "variantDbId", label: "Variant ID" },
-            { key: "variant_name", label: "变异名称" },
-            { key: "variant_type", label: "类型", render: (value) => optionLabel(variantTypeOptions, value) },
-            { key: "variant_set_name", label: "VariantSet" },
-            { key: "reference_set_name", label: "ReferenceSet" },
-            { key: "start", label: "起点" },
-            { key: "end", label: "终点" },
-            { key: "reference_bases", label: "参考碱基" },
-            { key: "filters_passed", label: "过滤", render: boolLabel },
-          ]}
-          fields={variantFields}
-          data={[]}
-          stats={[{ label: "/brapi/v2/variants", value: "BrAPI", className: "bg-rose-50 text-rose-700 dark:bg-rose-400/10 dark:text-rose-200" }]}
-          loadData={loadVariants}
-          createRecord={(payload) => createVariantRow(payload) as unknown as Promise<Record<string, unknown>>}
-          updateRecord={(id, payload) => updateVariantRow(id, payload) as unknown as Promise<Record<string, unknown>>}
-          deleteRecord={deleteVariantRow}
-        />
-      </TabsContent>
 
-      <TabsContent value="calls" className="mt-0 min-h-0 flex-1">
+      {tab === "calls" ? (
-        <BrapiEntityPage
+        <TabsContent value="calls" className="mt-0 min-h-0 flex-1">
-          useEnhancedDialog
+          <BrapiEntityPage
-          icon={Binary}
+            useEnhancedDialog
-          iconBg="bg-gradient-to-br from-sky-500 to-cyan-600"
+            icon={Binary}
-          title="Call 基因型判读"
+            iconBg="bg-gradient-to-br from-sky-500 to-cyan-600"
-          description="维护样品 CallSet 在指定 Variant 上的 genotype、深度和相位信息。"
+            title="Call 基因型判读"
-          addLabel="新增 Call"
+            description="维护样品 CallSet 在指定 Variant 上的 genotype、深度和相位信息。"
-          columns={[
+            addLabel="新增 Call"
-            { key: "callDbId", label: "Call ID" },
+            columns={[
-            { key: "call_set_name", label: "CallSet" },
+              { key: "callDbId", label: "Call ID" },
-            { key: "variant_name", label: "Variant" },
+              { key: "call_set_name", label: "CallSet" },
-            { key: "genotype_text", label: "Genotype" },
+              { key: "variant_name", label: "Variant" },
-            { key: "genotype_likelihood", label: "似然值" },
+              { key: "genotype_text", label: "Genotype" },
-            { key: "read_depth", label: "深度" },
+              { key: "genotype_likelihood", label: "似然值" },
-            { key: "phase_set", label: "Phase Set" },
+              { key: "read_depth", label: "深度" },
-          ]}
+              { key: "phase_set", label: "Phase Set" },
-          fields={callFields}
+            ]}
-          data={[]}
+            fields={callFields}
-          stats={[{ label: "/brapi/v2/calls", value: "BrAPI", className: "bg-sky-50 text-sky-700 dark:bg-sky-400/10 dark:text-sky-200" }]}
+            data={[]}
-          loadData={loadCalls}
+            stats={[{ label: "/brapi/v2/calls", value: "BrAPI", className: "bg-sky-50 text-sky-700 dark:bg-sky-400/10 dark:text-sky-200" }]}
-          createRecord={(payload) => createCallRow(payload) as unknown as Promise<Record<string, unknown>>}
+            loadData={loadCalls}
-          updateRecord={(id, payload) => updateCallRow(id, payload) as unknown as Promise<Record<string, unknown>>}
+            createRecord={(payload) => createCallRow(payload) as unknown as Promise<Record<string, unknown>>}
-          deleteRecord={deleteCallRow}
+            updateRecord={(id, payload) => updateCallRow(id, payload) as unknown as Promise<Record<string, unknown>>}
-        />
+            deleteRecord={deleteCallRow}
-      </TabsContent>
+          />
+        </TabsContent>
+      ) : null}
     </Tabs>
   );
 }

frontend/src/app/(app)/genotyping/variant/types.ts

@@ -5,6 +5,13 @@ export interface SelectOption {
   label: string;
 }
 
+export interface VariantQuery {
+  variant_name?: string;
+  variant_type?: string;
+  variant_set_id?: string;
+  reference_set_id?: string;
+}
+
 export interface ReferenceRecord {
   id: string;
   referenceId: string;
@@ -27,9 +34,10 @@ export interface VariantRecord {
   variantDbId: string;
   variantName: string | null;
   variant_name: string | null;
+  variantNames?: string[] | null;
   variantType: string | null;
   variant_type: string | null;
-  variantSetDbId: string | null;
+  variantSetDbId: string | string[] | null;
   variant_set_id: string | null;
   variantSetName: string | null;
   variant_set_name: string | null;
@@ -50,6 +58,7 @@ export interface VariantRecord {
   filters_applied: boolean | null;
   filtersPassed: boolean | null;
   filters_passed: boolean | null;
+  allele_call_count?: number | null;
 }
 
 export interface CallGenotype {

frontend/src/app/(app)/genotyping/variant/variants/[variantDbId]/page.tsx

@@ -0,0 +1,126 @@
+"use client";
+
+import Link from "next/link";
+import { useEffect, useState } from "react";
+import { useParams } from "next/navigation";
+import { ArrowLeft, MapPin, Sigma } from "lucide-react";
+import { Badge } from "@/components/ui/badge";
+import { Button } from "@/components/ui/button";
+import { Card, CardContent, CardHeader, CardTitle } from "@/components/ui/card";
+import { Skeleton } from "@/components/ui/skeleton";
+import { fetchVariantDetail } from "../../api";
+
+const boolLabel = (value: boolean | null | undefined) => {
+  if (value === true) return "是";
+  if (value === false) return "否";
+  return "N/A";
+};
+
+export default function VariantDetailPage() {
+  const params = useParams<{ variantDbId: string }>();
+  const variantDbId = decodeURIComponent(params.variantDbId);
+
+  const [loading, setLoading] = useState(true);
+  const [error, setError] = useState<string | null>(null);
+  const [detail, setDetail] = useState<Awaited<ReturnType<typeof fetchVariantDetail>> | null>(null);
+
+  useEffect(() => {
+    let mounted = true;
+    setLoading(true);
+    setError(null);
+    fetchVariantDetail(variantDbId)
+      .then((result) => {
+        if (!mounted) return;
+        setDetail(result);
+      })
+      .catch((event) => {
+        if (!mounted) return;
+        setError(event instanceof Error ? event.message : "加载 Variant 详情失败");
+      })
+      .finally(() => {
+        if (mounted) setLoading(false);
+      });
+    return () => { mounted = false; };
+  }, [variantDbId]);
+
+  if (loading) {
+    return (
+      <div className="space-y-4 p-1">
+        <Skeleton className="h-10 w-48" />
+        <Skeleton className="h-36 w-full" />
+      </div>
+    );
+  }
+
+  if (error || !detail) {
+    return (
+      <div className="rounded-xl border border-destructive/20 bg-destructive/10 px-4 py-6 text-sm text-destructive">
+        {error || "Variant 不存在"}
+        <div className="mt-4">
+          <Button asChild variant="outline">
+            <Link href="/genotyping/variant"><ArrowLeft className="mr-2 h-4 w-4" />返回列表</Link>
+          </Button>
+        </div>
+      </div>
+    );
+  }
+
+  return (
+    <div className="flex min-h-full flex-col gap-4">
+      <div className="flex flex-wrap items-center justify-between gap-3">
+        <Button asChild variant="outline" size="sm">
+          <Link href="/genotyping/variant"><ArrowLeft className="mr-2 h-4 w-4" />返回 Variant 列表</Link>
+        </Button>
+        {(detail.allele_call_count ?? 0) > 0 ? (
+          <Badge variant="outline" className="border-amber-200 bg-amber-50 text-amber-800 dark:border-amber-900 dark:bg-amber-950 dark:text-amber-200">
+            已有 {detail.allele_call_count} 条 allele_call，删除前请先处理关联数据
+          </Badge>
+        ) : null}
+      </div>
+
+      <Card>
+        <CardHeader className="pb-3">
+          <CardTitle className="flex items-center gap-2 text-lg">
+            <Sigma className="h-5 w-5 text-rose-500" />
+            {detail.variant_name || detail.id}
+          </CardTitle>
+        </CardHeader>
+        <CardContent className="grid gap-3 text-sm sm:grid-cols-2 lg:grid-cols-4">
+          <div><span className="text-slate-500">Variant ID：</span>{detail.id}</div>
+          <div><span className="text-slate-500">类型：</span>{detail.variant_type || "N/A"}</div>
+          <div><span className="text-slate-500">VariantSet：</span>{detail.variant_set_name || "N/A"}</div>
+          <div><span className="text-slate-500">ReferenceSet：</span>{detail.reference_set_name || "N/A"}</div>
+          <div><span className="text-slate-500">起点：</span>{detail.start ?? "N/A"}</div>
+          <div><span className="text-slate-500">终点：</span>{detail.end ?? "N/A"}</div>
+          <div><span className="text-slate-500">参考碱基：</span>{detail.reference_bases || "N/A"}</div>
+          <div><span className="text-slate-500">SV 长度：</span>{detail.svlen ?? "N/A"}</div>
+          <div><span className="text-slate-500">已应用过滤：</span>{boolLabel(detail.filters_applied)}</div>
+          <div><span className="text-slate-500">通过过滤：</span>{boolLabel(detail.filters_passed)}</div>
+          <div><span className="text-slate-500">allele_call 数：</span>{detail.allele_call_count ?? 0}</div>
+        </CardContent>
+      </Card>
+
+      <Card>
+        <CardHeader className="pb-3">
+          <CardTitle className="flex items-center gap-2 text-base">
+            <MapPin className="h-4 w-4 text-emerald-500" />
+            Marker Position
+          </CardTitle>
+        </CardHeader>
+        <CardContent className="text-sm text-slate-600 dark:text-slate-300">
+          <p>
+            Marker Position 与遗传图谱 linkage group 关联，可在后续 Marker / GenomeMap 模块中维护。
+            当前 Variant 详情已展示 allele_call 引用数量，便于删除前校验。
+          </p>
+          {detail.variant_set_id ? (
+            <Button asChild variant="link" className="mt-2 h-auto px-0 text-violet-600 dark:text-violet-400">
+              <Link href={`/genotyping/variant-set/variant-sets/${encodeURIComponent(detail.variant_set_id)}`}>
+                查看所属 VariantSet
+              </Link>
+            </Button>
+          ) : null}
+        </CardContent>
+      </Card>
+    </div>
+  );
+}

frontend/src/app/(app)/germplasm/breeding-method/api.ts

@@ -71,14 +71,14 @@ export const mapBreedingMethod = (method: BreedingMethod): BreedingMethodRecord
 };
 
 async function fetchBreedingMethodList(): Promise<BreedingMethod[]> {
-  const response = await request<BrapiListResponse<BreedingMethod>>("/brapi/v2/breedingmethods?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<BreedingMethod>>("/brapi/v2/breedingmethods?page=0&pageSize=10");
   return response.result?.data ?? [];
 }
 
 const toRequestBody = (payload: Record<string, unknown>) => {
   const breedingMethodName = emptyToNull(payload.breedingMethodName ?? payload.name);
   if (!breedingMethodName) {
-    throw new Error("请填写方法名称");
+    throw new Error("???????");
   }
   return {
     breedingMethodName,

frontend/src/app/(app)/germplasm/cross-pedigree/api.ts

@@ -105,7 +105,7 @@ const buildCrossParent = (
   const observationUnitDbId = optionalText(observationUnitId);
   if (!parentTypeValue && !germplasmDbId && !observationUnitDbId) return null;
   if (!parentTypeValue) throw new Error("请为已填亲本选择 parent_type");
-  if (!germplasmDbId && !observationUnitDbId) throw new Error("亲本必须填写 germplasm 或 observation_unit 至少一项");
+  if (!germplasmDbId && !observationUnitDbId) throw new Error("亲本必须填写 germplasm <EFBFBD>?observation_unit 至少一");
   return {
     parentType: parentTypeValue as CrossParent["parentType"],
     ...(germplasmDbId ? { germplasmDbId } : {}),
@@ -181,23 +181,23 @@ export function buildCrossParentFormState(
 }
 
 const crossingProjectBody = (payload: CrossingProjectPayload) => {
-  const programDbId = requiredText(payload.program_id, "请选择所属 Program");
+  const programDbId = requiredText(payload.program_id, "请选择所<EFBFBD>?Program");
   return {
-    crossingProjectName: requiredText(payload.name, "请填写杂交项目名称"),
+    crossingProjectName: requiredText(payload.name, "请填写杂交项目名"),
     crossingProjectDescription: optionalText(payload.description),
     programDbId,
   };
 };
 
 const plannedCrossBody = (payload: PlannedCrossPayload) => ({
-  plannedCrossName: requiredText(payload.name, "请填写计划杂交名称"),
+  plannedCrossName: requiredText(payload.name, "请填写计划杂交名"),
   crossingProjectDbId: requiredText(payload.crossing_project_id, "请选择杂交项目"),
   ...(optionalText(payload.cross_type) ? { crossType: optionalText(payload.cross_type) } : {}),
   ...(optionalText(payload.status) ? { status: optionalText(payload.status) } : { status: "TODO" }),
 });
 
 const crossBody = (payload: CrossPayload) => ({
-  crossName: requiredText(payload.name, "请填写实际杂交名称"),
+  crossName: requiredText(payload.name, "请填写实际杂交名"),
   crossingProjectDbId: requiredText(payload.crossing_project_id, "请选择杂交项目"),
   ...(optionalText(payload.cross_type) ? { crossType: optionalText(payload.cross_type) } : {}),
   ...(optionalText(payload.planned_cross_id) ? { plannedCrossDbId: optionalText(payload.planned_cross_id) } : {}),
@@ -430,7 +430,7 @@ export async function fetchCrossParentRows(): Promise<CrossParentRow[]> {
 }
 
 export async function updateCrossParents(payload: CrossParentFormState): Promise<void> {
-  const crossId = requiredText(payload.cross_id, "请选择所属 Cross");
+  const crossId = requiredText(payload.cross_id, "请选择所<EFBFBD>?Cross");
   const parent1 = buildCrossParent(
     payload.parent1_type,
     payload.parent1_germplasm_id,
@@ -466,14 +466,14 @@ export async function updateCrossParents(payload: CrossParentFormState): Promise
 
 export async function fetchPedigreeRows(): Promise<PedigreeRecord[]> {
   const response = await request<BrapiListResponse<PedigreeRecord & PedigreeNode>>(
-    "/brapi/v2/pedigree?page=0&pageSize=1000",
+    "/brapi/v2/pedigree?page=0&pageSize=10",
   );
   return response.result.data.map(mapPedigree);
 }
 
 export async function fetchPedigreeRowsWithRelations(): Promise<PedigreeRecord[]> {
   const response = await request<BrapiListResponse<PedigreeRecord & PedigreeNode>>(
-    "/brapi/v2/pedigree?page=0&pageSize=1000&includeParents=true&includeProgeny=false&includeSiblings=true",
+    "/brapi/v2/pedigree?page=0&pageSize=10&includeParents=true&includeProgeny=false&includeSiblings=true",
   );
   return response.result.data.map(mapPedigree);
 }
@@ -481,7 +481,7 @@ export async function fetchPedigreeRowsWithRelations(): Promise<PedigreeRecord[]
 export async function fetchPedigreeDetail(id: string): Promise<PedigreeRecord> {
   const rows = await fetchPedigreeRows();
   const found = rows.find((row) => row.id === id || row.germplasm_id === id);
-  if (!found) throw new Error("系谱节点不存在");
+  if (!found) throw new Error("系谱节点不存");
   return found;
 }
 
@@ -526,7 +526,7 @@ export async function upsertPedigreeEdge(payload: PedigreeEdgeFormState, origina
   const thisNodeId = requiredText(payload.this_node_id, "请选择当前材料");
   const connectedNodeId = requiredText(payload.connected_node_id, "请选择关联材料");
   if (thisNodeId === connectedNodeId) {
-    throw new Error("当前材料与关联材料不能相同");
+    throw new Error("当前材料与关联材料不能相");
   }
   if (edgeType === "sibling") {
     throw new Error("同胞关系由共享亲本自动推断，请通过 parent 关系维护");
@@ -560,7 +560,7 @@ export async function upsertPedigreeEdge(payload: PedigreeEdgeFormState, origina
 export async function removePedigreeEdge(edgeId: string): Promise<void> {
   const [edgeType, thisNodeId, connectedNodeId] = edgeId.split(":");
   if (edgeType !== "parent" || !thisNodeId || !connectedNodeId) {
-    throw new Error("仅支持删除 parent 关系");
+    throw new Error("仅支持删<EFBFBD>?parent 关系");
   }
 
   const nodes = await fetchPedigreeRowsWithRelations();

frontend/src/app/(app)/germplasm/cross-pedigree/crossPedigreeCache.ts

@@ -118,9 +118,9 @@ async function fetchSnapshotFromNetwork(): Promise<CrossPedigreeSnapshot> {
   const [programs, germplasm, crossingProjects, plannedCrosses, actualCrosses, observationUnits] = await Promise.all([
     loadProgramOptions(),
     loadGermplasmOptions(),
-    request<BrapiListResponse<CrossingProject>>("/brapi/v2/crossingprojects?page=0&pageSize=1000"),
+    request<BrapiListResponse<CrossingProject>>("/brapi/v2/crossingprojects?page=0&pageSize=10"),
-    request<BrapiListResponse<PlannedCross>>("/brapi/v2/plannedcrosses?page=0&pageSize=1000"),
+    request<BrapiListResponse<PlannedCross>>("/brapi/v2/plannedcrosses?page=0&pageSize=10"),
-    request<BrapiListResponse<Cross>>("/brapi/v2/crosses?page=0&pageSize=1000"),
+    request<BrapiListResponse<Cross>>("/brapi/v2/crosses?page=0&pageSize=10"),
     loadObservationUnitOptions().catch(() => [] as SelectOption[]),
   ]);
 

frontend/src/app/(app)/germplasm/germplasm/api.ts

@@ -99,7 +99,7 @@ const optionalNumber = (value: unknown) => {
 
 const germplasmName = (payload: GermplasmPayload) => {
   const name = optionalText(payload.germplasm_name);
-  if (!name) throw new Error("请填写种质名称");
+  if (!name) throw new Error("请填写种质名");
   return name;
 };
 
@@ -154,7 +154,7 @@ const toRequestBody = (payload: GermplasmPayload) => ({
 });
 
 export async function fetchGermplasmRows(): Promise<GermplasmRecord[]> {
-  const response = await request<BrapiListResponse<GermplasmRecord>>("/brapi/v2/germplasm?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<GermplasmRecord>>("/brapi/v2/germplasm?page=0&pageSize=10");
   return response.result.data.map(mapGermplasm);
 }
 

frontend/src/app/(app)/germplasm/germplasm/attributeApi.ts

@@ -105,7 +105,7 @@ export function normalizeAttributeFormData(record: AttributeRecord): Record<stri
 
 const toRequestBody = (payload: AttributePayload) => {
   const attributeName = optionalText(payload.attributeName);
-  if (!attributeName) throw new Error("请填写属性名称");
+  if (!attributeName) throw new Error("请填写属性名");
 
   const dataType = optionalText(payload.dataType) as AttributeDataType | null;
   const scaleName = `${attributeName} scale`;
@@ -128,7 +128,7 @@ const toRequestBody = (payload: AttributePayload) => {
 };
 
 export async function fetchAttributeRows(): Promise<AttributeRecord[]> {
-  const response = await request<BrapiListResponse<GermplasmAttribute>>("/brapi/v2/attributes?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<GermplasmAttribute>>("/brapi/v2/attributes?page=0&pageSize=10");
   return (response.result?.data ?? []).map(mapAttribute);
 }
 
@@ -150,7 +150,7 @@ export async function fetchAttributeOptions(): Promise<SelectOption[]> {
 }
 
 export async function fetchAttributeFormOptions(): Promise<{ crops: SelectOption[] }> {
-  const cropsResult = await request<CommonCropNamesResponse>("/brapi/v2/commoncropnames?page=0&pageSize=1000").catch(() => null);
+  const cropsResult = await request<CommonCropNamesResponse>("/brapi/v2/commoncropnames?page=0&pageSize=10").catch(() => null);
   return {
     crops: (cropsResult?.result?.data ?? []).map((cropName) => ({
       value: cropName,

frontend/src/app/(app)/germplasm/germplasm/attributeValueApi.ts

@@ -103,9 +103,9 @@ const toRequestBody = (payload: AttributeValuePayload) => {
   const germplasmDbId = optionalText(payload.germplasm_id);
   const value = optionalText(payload.value);
 
-  if (!attributeDbId) throw new Error("请选择属性定义");
+  if (!attributeDbId) throw new Error("请选择属性定");
   if (!germplasmDbId) throw new Error("请选择种质材料");
-  if (!value) throw new Error("请填写属性值");
+  if (!value) throw new Error("请填写属性");
 
   return {
     attributeDbId,
@@ -119,8 +119,8 @@ const toRequestBody = (payload: AttributeValuePayload) => {
 
 export async function fetchAttributeValueRows(germplasmDbId?: string): Promise<AttributeValueRecord[]> {
   const query = germplasmDbId
-    ? `?page=0&pageSize=1000&germplasmDbId=${encodeURIComponent(germplasmDbId)}`
+    ? `?page=0&pageSize=10&germplasmDbId=${encodeURIComponent(germplasmDbId)}`
-    : "?page=0&pageSize=1000";
+    : "?page=0&pageSize=10";
   const response = await request<BrapiListResponse<GermplasmAttributeValue>>(`/brapi/v2/attributevalues${query}`);
   return (response.result?.data ?? []).map(mapAttributeValue);
 }

frontend/src/app/(app)/germplasm/seed-lot/api.ts

@@ -109,7 +109,7 @@ const optionalNumber = (value: unknown) => {
 
 const seedLotName = (payload: SeedLotPayload) => {
   const name = optionalText(payload.name);
-  if (!name) throw new Error("请填写批次名称");
+  if (!name) throw new Error("请填写批次名");
   return name;
 };
 
@@ -145,7 +145,7 @@ export const buildContentMixturePayload = (payload: SeedLotPayload) => {
   }
 
   if (rows.length === 0) {
-    throw new Error("请至少录入一条批次组成，或选择主材料");
+    throw new Error("请至少录入一条批次组成，或选择主材");
   }
 
   const normalized = rows.map((row) => {
@@ -154,10 +154,10 @@ export const buildContentMixturePayload = (payload: SeedLotPayload) => {
     const mixturePercentage = optionalNumber(row.mixture_percentage);
 
     if (!germplasmDbId && !crossDbId) {
-      throw new Error("批次组成每行需选择材料或杂交来源");
+      throw new Error("批次组成每行需选择材料或杂交来");
     }
     if (mixturePercentage === null || mixturePercentage < 0 || mixturePercentage > 100) {
-      throw new Error("批次组成占比需在 0 到 100 之间");
+      throw new Error("批次组成占比需<EFBFBD>?0 <20>?100 之间");
     }
 
     return {
@@ -268,7 +268,7 @@ export function normalizeSeedLotFormData(record: SeedLotRecord): Record<string,
 }
 
 const seedLotRowsLoader = createCachedLoader(async () => {
-  const response = await request<BrapiListResponse<SeedLotRecord>>("/brapi/v2/seedlots?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<SeedLotRecord>>("/brapi/v2/seedlots?page=0&pageSize=10");
   return response.result.data.map(mapSeedLot);
 });
 
@@ -349,8 +349,8 @@ export async function fetchSeedLotTransactions(seedLotDbId?: string): Promise<Se
   const [transactionsResponse, seedLots] = await Promise.all([
     request<BrapiListResponse<SeedLotTransactionRecord>>(
       seedLotDbId
-        ? `/brapi/v2/seedlots/${encodeURIComponent(seedLotDbId)}/transactions?page=0&pageSize=1000`
+        ? `/brapi/v2/seedlots/${encodeURIComponent(seedLotDbId)}/transactions?page=0&pageSize=10`
-        : "/brapi/v2/seedlots/transactions?page=0&pageSize=1000",
+        : "/brapi/v2/seedlots/transactions?page=0&pageSize=10",
     ),
     fetchSeedLotRows().catch(() => [] as SeedLotRecord[]),
   ]);
@@ -365,7 +365,7 @@ export function inferTransactionAction(transaction: SeedLotTransactionRecord): T
   if (!fromId && toId) return "in";
   if (fromId && !toId) {
     const description = String(transaction.description ?? "").toLowerCase();
-    if (description.includes("报废") || description.includes("消耗")) return "consume";
+    if (description.includes("报废") || description.includes("消")) return "consume";
     return "out";
   }
   if (fromId && toId) {
@@ -388,7 +388,7 @@ export async function createSeedLotTransaction(payload: TransactionPayload, seed
   const toId = optionalText(payload.to_seed_lot_id);
 
   if (fromId && toId && fromId === toId) {
-    throw new Error("来源批次与目标批次不能相同");
+    throw new Error("来源批次与目标批次不能相");
   }
 
   let fromSeedLotDbId: string | undefined;
@@ -405,38 +405,38 @@ export async function createSeedLotTransaction(payload: TransactionPayload, seed
     case "consume":
       if (!fromId) throw new Error("出库/消耗需选择来源批次");
       if ((payload.action === "out" || payload.action === "consume") && !description) {
-        throw new Error("出库/消耗/报废建议填写流转说明");
+        throw new Error("出库/消<EFBFBD>?报废建议填写流转说明");
       }
       fromSeedLotDbId = fromId;
       units = units || seedLotMap.get(fromId)?.units || null;
       break;
     case "transfer":
     case "split":
-      if (!fromId || !toId) throw new Error("转移/分装需同时选择来源与目标批次");
+      if (!fromId || !toId) throw new Error("转移/分装需同时选择来源与目标批");
       fromSeedLotDbId = fromId;
       toSeedLotDbId = toId;
       units = units || seedLotMap.get(fromId)?.units || seedLotMap.get(toId)?.units || null;
       break;
     default:
-      throw new Error("未知的库存动作");
+      throw new Error("未知的库存动");
   }
 
   if (!fromSeedLotDbId && !toSeedLotDbId) {
-    throw new Error("来源批次与目标批次至少填写一个");
+    throw new Error("来源批次与目标批次至少填写一");
   }
 
   const sourceLot = fromSeedLotDbId ? seedLotMap.get(fromSeedLotDbId) : undefined;
   if (fromSeedLotDbId && sourceLot) {
     const currentAmount = Number(sourceLot.amount ?? 0);
     if (amount > currentAmount) {
-      throw new Error(`出库数量不能超过当前库存（${currentAmount}${sourceLot.units ? ` ${sourceLot.units}` : ""}）`);
+      throw new Error(`出库数量不能超过当前库存：${currentAmount}${sourceLot.units ? ` ${sourceLot.units}` : ""}）`);
     }
   }
 
-  if (!units) throw new Error("请指定流转单位");
+  if (!units) throw new Error("请指定流转单");
 
-  const transactionDescription = payload.action === "consume" && description && !description.includes("消耗")
+  const transactionDescription = payload.action === "consume" && description && !description.includes("消")
-    ? `消耗/报废：${description}`
+    ? `消<EFBFBD>?报废：${description}`
     : payload.action === "split" && description && !description.includes("分装")
       ? `分装：${description}`
       : description;

frontend/src/app/(app)/phenotyping/event-image/api.ts

@@ -183,12 +183,12 @@ const imageBody = (payload: ImagePayload) => ({
 });
 
 export async function fetchEventRows(): Promise<EventRecord[]> {
-  const response = await request<BrapiListResponse<EventRecord>>("/brapi/v2/events?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<EventRecord>>("/brapi/v2/events?page=0&pageSize=10");
   return response.result.data.map(mapEvent);
 }
 
 export async function fetchImageRows(): Promise<ImageRecord[]> {
-  const response = await request<BrapiListResponse<ImageRecord>>("/brapi/v2/images?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<ImageRecord>>("/brapi/v2/images?page=0&pageSize=10");
   return response.result.data.map(mapImage);
 }
 
@@ -198,9 +198,9 @@ export async function fetchEventImageOptions(): Promise<{
   observations: SelectOption[];
 }> {
   const [studies, observationUnits, observations] = await Promise.all([
-    request<BrapiListResponse<StudyResponse>>("/brapi/v2/studies?page=0&pageSize=1000"),
+    request<BrapiListResponse<StudyResponse>>("/brapi/v2/studies?page=0&pageSize=10"),
-    request<BrapiListResponse<ObservationUnitResponse>>("/brapi/v2/observationunits?page=0&pageSize=1000"),
+    request<BrapiListResponse<ObservationUnitResponse>>("/brapi/v2/observationunits?page=0&pageSize=10"),
-    request<BrapiListResponse<ObservationResponse>>("/brapi/v2/observations?page=0&pageSize=1000"),
+    request<BrapiListResponse<ObservationResponse>>("/brapi/v2/observations?page=0&pageSize=10"),
   ]);
 
   return {

frontend/src/app/(app)/phenotyping/observation-unit/api.ts

@@ -101,7 +101,7 @@ const mapObservationUnit = (unit: ObservationUnitRecord): ObservationUnitRecord
 };
 
 const toRequestBody = (payload: ObservationUnitPayload) => ({
-  observationUnitName: requiredText(payload.observation_unit_name, "请填写观测单元名称"),
+  observationUnitName: requiredText(payload.observation_unit_name, "请填写观测单元名"),
   studyDbId: optionalText(payload.study_id),
   germplasmDbId: optionalText(payload.germplasm_id),
   observationLevel: {
@@ -113,7 +113,7 @@ const toRequestBody = (payload: ObservationUnitPayload) => ({
 });
 
 export async function fetchObservationUnitRows(): Promise<ObservationUnitRecord[]> {
-  const response = await request<BrapiListResponse<ObservationUnitRecord>>("/brapi/v2/observationunits?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<ObservationUnitRecord>>("/brapi/v2/observationunits?page=0&pageSize=10");
   return response.result.data.map(mapObservationUnit);
 }
 
@@ -133,7 +133,7 @@ export async function createObservationUnitRow(payload: ObservationUnitPayload):
   const response = await request<BrapiListResponse<ObservationUnitRecord>>("/brapi/v2/observationunits", {
     method: "POST",
     body: JSON.stringify({
-      observationUnitDbId: requiredText(payload.id, "请填写观测单元 ID"),
+      observationUnitDbId: requiredText(payload.id, "请填写观测单<EFBFBD>?ID"),
       ...toRequestBody(payload),
     }),
   });

frontend/src/app/(app)/phenotyping/observation-variable/api.ts

@@ -136,7 +136,7 @@ const mapObservationVariable = (variable: ObservationVariableRecord): Observatio
 });
 
 const toRequestBody = (payload: ObservationVariablePayload) => ({
-  observationVariableName: requiredText(payload.name, "请填写变量名称"),
+  observationVariableName: requiredText(payload.name, "请填写变量名"),
   pui: optionalText(payload.pui),
   defaultValue: optionalText(payload.default_value),
   documentationurl: optionalText(payload.documentationurl),
@@ -154,7 +154,7 @@ const toRequestBody = (payload: ObservationVariablePayload) => ({
 });
 
 export async function fetchObservationVariableRows(): Promise<ObservationVariableRecord[]> {
-  const response = await request<BrapiListResponse<ObservationVariableRecord>>("/brapi/v2/variables?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<ObservationVariableRecord>>("/brapi/v2/variables?page=0&pageSize=10");
   return response.result.data.map(mapObservationVariable);
 }
 
@@ -167,10 +167,10 @@ export async function fetchObservationVariableOptions(): Promise<{
 }> {
   const [crops, ontologies, traits, methods, scales] = await Promise.all([
     request<CropResponse[]>("/api/dictionaries/crops"),
-    request<BrapiListResponse<OntologyResponse>>("/brapi/v2/ontologies?page=0&pageSize=1000"),
+    request<BrapiListResponse<OntologyResponse>>("/brapi/v2/ontologies?page=0&pageSize=10"),
-    request<BrapiListResponse<TraitResponse>>("/brapi/v2/traits?page=0&pageSize=1000"),
+    request<BrapiListResponse<TraitResponse>>("/brapi/v2/traits?page=0&pageSize=10"),
-    request<BrapiListResponse<MethodResponse>>("/brapi/v2/methods?page=0&pageSize=1000"),
+    request<BrapiListResponse<MethodResponse>>("/brapi/v2/methods?page=0&pageSize=10"),
-    request<BrapiListResponse<ScaleResponse>>("/brapi/v2/scales?page=0&pageSize=1000"),
+    request<BrapiListResponse<ScaleResponse>>("/brapi/v2/scales?page=0&pageSize=10"),
   ]);
 
   return {
@@ -201,7 +201,7 @@ export async function createObservationVariableRow(payload: ObservationVariableP
   const response = await request<BrapiListResponse<ObservationVariableRecord>>("/brapi/v2/variables", {
     method: "POST",
     body: JSON.stringify({
-      id: requiredText(payload.id, "请填写变量 ID"),
+      id: requiredText(payload.id, "请填写变<EFBFBD>?ID"),
       ...toRequestBody(payload),
     }),
   });

frontend/src/app/(app)/project/program/api.ts

@@ -77,7 +77,7 @@ const optionalNumber = (value: unknown) => {
 
 const programName = (payload: ProgramPayload) => {
   const name = optionalText(payload.name);
-  if (!name) throw new Error("请填写项目名称");
+  if (!name) throw new Error("请填写项目名");
   return name;
 };
 
@@ -106,7 +106,7 @@ const toRequestBody = (payload: ProgramPayload) => ({
 });
 
 export async function fetchProgramRows(): Promise<ProgramRecord[]> {
-  const response = await request<BrapiListResponse<ProgramRecord>>("/brapi/v2/programs?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<ProgramRecord>>("/brapi/v2/programs?page=0&pageSize=10");
   return response.result.data.map(mapProgram);
 }
 

frontend/src/app/(app)/project/study/api.ts

@@ -137,7 +137,7 @@ const optionalBoolean = (value: unknown) => {
 
 const studyName = (payload: StudyPayload) => {
   const name = optionalText(payload.study_name);
-  if (!name) throw new Error("请填写研究名称");
+  if (!name) throw new Error("请填写研究名");
   return name;
 };
 
@@ -241,7 +241,7 @@ const toRequestBody = (payload: StudyPayload & Record<string, unknown>) => {
 };
 
 export async function fetchStudyRows(): Promise<StudyRecord[]> {
-  const response = await request<BrapiListResponse<Study>>("/brapi/v2/studies?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<Study>>("/brapi/v2/studies?page=0&pageSize=10");
   return response.result.data.map(mapStudy);
 }
 
@@ -251,7 +251,7 @@ export async function fetchStudyDetail(studyDbId: string): Promise<StudyRecord>
 }
 
 const studyTrialOptionsLoader = createCachedLoader(async () => {
-  const response = await request<BrapiListResponse<TrialResponse>>("/brapi/v2/trials?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<TrialResponse>>("/brapi/v2/trials?page=0&pageSize=10");
   return response.result.data.map((trial) => ({
     value: trial.trialDbId,
     label: `${trial.trialName || trial.trial_name || trial.trialDbId}${trial.programName || trial.program_name ? ` / ${trial.programName || trial.program_name}` : ""}`,

frontend/src/app/(app)/project/trial/api.ts

@@ -104,7 +104,7 @@ const optionalBoolean = (value: unknown) => {
 
 const trialName = (payload: TrialPayload) => {
   const name = optionalText(payload.trial_name);
-  if (!name) throw new Error("请填写试验名称");
+  if (!name) throw new Error("请填写试验名");
   return name;
 };
 
@@ -164,7 +164,7 @@ const toRequestBody = (payload: TrialPayload) => {
 };
 
 export async function fetchTrialRows(): Promise<TrialRecord[]> {
-  const response = await request<BrapiListResponse<Trial>>("/brapi/v2/trials?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<Trial>>("/brapi/v2/trials?page=0&pageSize=10");
   return response.result.data.map(mapTrial);
 }
 

frontend/src/components/brapi/BrapiEntityPage.tsx

@@ -252,6 +252,12 @@ export function BrapiEntityPage({
     ?? row.crossDbId
     ?? row.plateDbId
     ?? row.sampleDbId
+    ?? row.referenceSetDbId
+    ?? row.referenceDbId
+    ?? row.referenceBasesDbId
+    ?? row.variantSetDbId
+    ?? row.variantDbId
+    ?? row.callDbId
     ?? "",
   ), []);
 

frontend/src/components/brapi/navigation.ts

@@ -137,9 +137,15 @@ export const brapiNavSections: BrapiNavSection[] = [
       { title: "样品管理", items: [{ title: "Sample / Plate", href: "/genotyping/sample-plate", icon: TestTube }] },
       {
         title: "参考基因组",
-        items: [{ title: "ReferenceSet / Reference / Bases", href: "/genotyping/reference-set", icon: BookOpen }],
+        items: [{ title: "ReferenceSet / Reference", href: "/genotyping/reference-set", icon: BookOpen }],
+      },
+      {
+        title: "变异数据",
+        items: [
+          { title: "VariantSet", href: "/genotyping/variant-set", icon: Layers },
+          { title: "Variant / Call", href: "/genotyping/variant", icon: Sigma },
+        ],
       },
-      { title: "变异数据", items: [{ title: "Variant / Call", href: "/genotyping/variant", icon: Sigma }] },
     ],
   },
   {

frontend/src/constants/api.ts

@@ -0,0 +1,11 @@
+/** 前端列表/下拉 BrAPI 查询默认每页条数 */
+export const DEFAULT_LIST_PAGE_SIZE = 10;
+
+export const DEFAULT_LIST_PAGE = 0;
+
+/** 标准分页查询串：page=0&pageSize=10 */
+export const DEFAULT_PAGE_QUERY = `page=${DEFAULT_LIST_PAGE}&pageSize=${DEFAULT_LIST_PAGE_SIZE}`;
+
+export function buildPageQuery(page = DEFAULT_LIST_PAGE, pageSize = DEFAULT_LIST_PAGE_SIZE): string {
+  return `page=${page}&pageSize=${pageSize}`;
+}

frontend/src/constants/menu.ts

@@ -84,7 +84,10 @@ export const mockBackendMenus: BackendMenuResponse[] = [
     children: [
       { title: "样品管理", path: "/genotyping/sample", menu_type: "folder", icon: "test-tube", order_index: 1, children: [{ title: "Sample / Plate", path: "/genotyping/sample-plate", menu_type: "menu", icon: "test-tube", order_index: 1, children: [] }] },
       { title: "参考基因组", path: "/genotyping/reference", menu_type: "folder", icon: "book-open", order_index: 2, children: [{ title: "ReferenceSet / Reference / Bases", path: "/genotyping/reference-set", menu_type: "menu", icon: "book-open", order_index: 1, children: [] }] },
-      { title: "变异数据", path: "/genotyping/variant-group", menu_type: "folder", icon: "sigma", order_index: 3, children: [{ title: "Variant / Call", path: "/genotyping/variant", menu_type: "menu", icon: "sigma", order_index: 1, children: [] }] }
+      { title: "变异数据", path: "/genotyping/variant-group", menu_type: "folder", icon: "sigma", order_index: 3, children: [
+        { title: "VariantSet", path: "/genotyping/variant-set", menu_type: "menu", icon: "layers", order_index: 1, children: [] },
+        { title: "Variant / Call", path: "/genotyping/variant", menu_type: "menu", icon: "sigma", order_index: 2, children: [] },
+      ] }
     ]
   },
   {

frontend/src/lib/api/types.gen.ts

@@ -3342,9 +3342,11 @@ export type TraitsTraitDbIdDeleteResponses = {
     /**
      * OK
      */
-    200: unknown;
+    200: TraitSingleResponse;
 };
 
+export type TraitsTraitDbIdDeleteResponse = TraitsTraitDbIdDeleteResponses[keyof TraitsTraitDbIdDeleteResponses];
+
 export type TraitsTraitDbIdGetData = {
     body?: never;
     headers?: {

frontend/src/services/dictionaryService.ts

@@ -1,4 +1,5 @@
-import { getAuthToken } from "@/utils/token";
+import { DEFAULT_LIST_PAGE, DEFAULT_LIST_PAGE_SIZE } from "@/constants/api";
+import { getAuthToken } from "@/utils/token";
 
 export interface CropRecord {
   id: string;
@@ -141,7 +142,7 @@ async function request<T>(path: string, init?: RequestInit): Promise<T> {
 
   if (!response.ok) {
     const detail = await response.text();
-    throw new Error(detail || `请求失败：${response.status}`);
+    throw new Error(detail || `请求失败<EFBFBD><EFBFBD>?${response.status}`);
   }
   return response.json() as Promise<T>;
 }
@@ -160,7 +161,7 @@ export async function listCountries(keyword?: string): Promise<CountryRecord[]>
   return request<CountryRecord[]>(`/api/dictionaries/countries?${params.toString()}`);
 }
 
-export async function listCrops(page = 0, pageSize = 10): Promise<CropRecord[]> {
+export async function listCrops(page = DEFAULT_LIST_PAGE, pageSize = DEFAULT_LIST_PAGE_SIZE): Promise<CropRecord[]> {
   const encodedPage = encodeURIComponent(String(page));
   const encodedPageSize = encodeURIComponent(String(pageSize));
   const response = await request<BrapiListResponse<string>>(`/brapi/v2/commoncropnames?page=${encodedPage}&pageSize=${encodedPageSize}`);
@@ -278,7 +279,7 @@ export function deleteSeason(seasonDbId: string) {
   }).then(() => undefined);
 }
 
-export function listLocations(page = 0, pageSize = 1000) {
+export function listLocations(page = DEFAULT_LIST_PAGE, pageSize = DEFAULT_LIST_PAGE_SIZE) {
   const encodedPage = encodeURIComponent(String(page));
   const encodedPageSize = encodeURIComponent(String(pageSize));
   return request<BrapiListResponse<Omit<LocationRecord, "id">>>(
@@ -329,7 +330,7 @@ export function deleteLocation(locationDbId: string) {
   }).then(() => undefined);
 }
 
-export function listOntologies(page = 0, pageSize = 1000) {
+export function listOntologies(page = DEFAULT_LIST_PAGE, pageSize = DEFAULT_LIST_PAGE_SIZE) {
   const encodedPage = encodeURIComponent(String(page));
   const encodedPageSize = encodeURIComponent(String(pageSize));
   return request<BrapiListResponse<Omit<OntologyRecord, "id">>>(
@@ -372,7 +373,7 @@ const toOntologyRequestBody = (payload: OntologyPayload) => ({
 export function createOntology(payload: OntologyPayload) {
   const body = toOntologyRequestBody(payload);
   if (!body.ontologyName) {
-    return Promise.reject(new Error("请填写本体名称"));
+    return Promise.reject(new Error("请填写本体名<EFBFBD><EFBFBD>?"));
   }
   return request<BrapiListResponse<Omit<OntologyRecord, "id">>>("/brapi/v2/ontologies", {
     method: "POST",
@@ -380,7 +381,7 @@ export function createOntology(payload: OntologyPayload) {
   }).then((response) => {
     const ontology = response.result.data[0];
     if (!ontology) {
-      throw new Error("新增本体失败：后端未返回数据");
+      throw new Error("新<EFBFBD>?<3F>本体失败：后<EFBFBD>??<3F><>?返回数据");
     }
     return {
       ...ontology,

frontend/src/services/dropdownCache.ts

@@ -1,3 +1,4 @@
+import { DEFAULT_PAGE_QUERY } from "@/constants/api";
 import { getAuthToken } from "@/utils/token";
 
 export interface SelectOption {
@@ -73,7 +74,7 @@ interface BreedingMethodResponse {
   abbreviation: string | null;
 }
 
-const PAGE_QUERY = "page=0&pageSize=1000";
+const PAGE_QUERY = DEFAULT_PAGE_QUERY;
 
 const apiBase = () => {
   if (typeof window !== "undefined") return "";
@@ -93,7 +94,7 @@ async function request<T>(path: string, init?: RequestInit): Promise<T> {
 
   if (!response.ok) {
     const detail = await response.text();
-    throw new Error(detail || `请求失败：${response.status}`);
+    throw new Error(detail || `?????${response.status}`);
   }
   return response.json() as Promise<T>;
 }
@@ -297,7 +298,7 @@ export function invalidateAllDropdownCache() {
   commonCropNameLoader.invalidate();
 }
 
-/** 并行加载多个下拉，共享 in-flight 去重 */
+/** ??????????? in-flight ?? */
 export async function loadDropdownBundle(keys: {
   locations?: boolean;
   programs?: boolean;

src/main/java/org/brapi/test/BrAPITestServer/controller/geno/GenotypingVariantWriteController.java

@@ -0,0 +1,131 @@
+package org.brapi.test.BrAPITestServer.controller.geno;
+
+import java.util.List;
+
+import org.brapi.test.BrAPITestServer.controller.core.BrAPIController;
+import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerException;
+import org.brapi.test.BrAPITestServer.model.dto.geno.VariantSetWriteRequest;
+import org.brapi.test.BrAPITestServer.model.dto.geno.VariantWriteRequest;
+import org.brapi.test.BrAPITestServer.service.geno.VariantService;
+import org.brapi.test.BrAPITestServer.service.geno.VariantSetService;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.CrossOrigin;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestHeader;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RestController;
+
+import io.swagger.model.geno.Variant;
+import io.swagger.model.geno.VariantSet;
+import io.swagger.model.geno.VariantSetResponse;
+import io.swagger.model.geno.VariantSetsListResponse;
+import io.swagger.model.geno.VariantSetsListResponseResult;
+import io.swagger.model.geno.VariantSingleResponse;
+import io.swagger.model.geno.VariantsListResponse;
+import io.swagger.model.geno.VariantsListResponseResult;
+import jakarta.servlet.http.HttpServletRequest;
+
+@RestController
+public class GenotypingVariantWriteController extends BrAPIController {
+
+	private static final Logger log = LoggerFactory.getLogger(GenotypingVariantWriteController.class);
+
+	private final VariantSetService variantSetService;
+	private final VariantService variantService;
+	private final HttpServletRequest request;
+
+	@Autowired
+	public GenotypingVariantWriteController(VariantSetService variantSetService, VariantService variantService,
+			HttpServletRequest request) {
+		this.variantSetService = variantSetService;
+		this.variantService = variantService;
+		this.request = request;
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/variantsets", produces = { "application/json" }, consumes = {
+			"application/json" }, method = RequestMethod.POST)
+	public ResponseEntity<VariantSetsListResponse> variantSetsPost(@RequestBody VariantSetWriteRequest body,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		VariantSet data = variantSetService.saveVariantSet(body);
+		return responseOK(new VariantSetsListResponse(), new VariantSetsListResponseResult(), List.of(data));
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/variantsets/{variantSetDbId}", produces = { "application/json" }, consumes = {
+			"application/json" }, method = RequestMethod.PUT)
+	public ResponseEntity<VariantSetResponse> variantSetsVariantSetDbIdPut(
+			@PathVariable("variantSetDbId") String variantSetDbId, @RequestBody VariantSetWriteRequest body,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		VariantSet data = variantSetService.updateVariantSet(variantSetDbId, body);
+		return responseOK(new VariantSetResponse(), data);
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/variantsets/{variantSetDbId}", produces = {
+			"application/json" }, method = RequestMethod.DELETE)
+	public ResponseEntity<VariantSetResponse> variantSetsVariantSetDbIdDelete(
+			@PathVariable("variantSetDbId") String variantSetDbId,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		VariantSet data = variantSetService.deleteVariantSet(variantSetDbId);
+		return responseOK(new VariantSetResponse(), data);
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/variants", produces = { "application/json" }, consumes = {
+			"application/json" }, method = RequestMethod.POST)
+	public ResponseEntity<VariantsListResponse> variantsPost(@RequestBody VariantWriteRequest body,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		Variant data = variantService.saveVariant(body);
+		return responseOK(new VariantsListResponse(), new VariantsListResponseResult(), List.of(data));
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/variants/{variantDbId}", produces = { "application/json" }, consumes = {
+			"application/json" }, method = RequestMethod.PUT)
+	public ResponseEntity<VariantSingleResponse> variantsVariantDbIdPut(
+			@PathVariable("variantDbId") String variantDbId, @RequestBody VariantWriteRequest body,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		Variant data = variantService.updateVariant(variantDbId, body);
+		return responseOK(new VariantSingleResponse(), data);
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/variants/{variantDbId}", produces = {
+			"application/json" }, method = RequestMethod.DELETE)
+	public ResponseEntity<VariantSingleResponse> variantsVariantDbIdDelete(
+			@PathVariable("variantDbId") String variantDbId,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		Variant data = variantService.deleteVariant(variantDbId);
+		return responseOK(new VariantSingleResponse(), data);
+	}
+}

src/main/java/org/brapi/test/BrAPITestServer/model/dto/geno/VariantSetWriteRequest.java

@@ -0,0 +1,40 @@
+package org.brapi.test.BrAPITestServer.model.dto.geno;
+
+public class VariantSetWriteRequest {
+    private String variantSetDbId;
+    private String variantSetName;
+    private String referenceSetDbId;
+    private String studyDbId;
+
+    public String getVariantSetDbId() {
+        return variantSetDbId;
+    }
+
+    public void setVariantSetDbId(String variantSetDbId) {
+        this.variantSetDbId = variantSetDbId;
+    }
+
+    public String getVariantSetName() {
+        return variantSetName;
+    }
+
+    public void setVariantSetName(String variantSetName) {
+        this.variantSetName = variantSetName;
+    }
+
+    public String getReferenceSetDbId() {
+        return referenceSetDbId;
+    }
+
+    public void setReferenceSetDbId(String referenceSetDbId) {
+        this.referenceSetDbId = referenceSetDbId;
+    }
+
+    public String getStudyDbId() {
+        return studyDbId;
+    }
+
+    public void setStudyDbId(String studyDbId) {
+        this.studyDbId = studyDbId;
+    }
+}

src/main/java/org/brapi/test/BrAPITestServer/model/dto/geno/VariantWriteRequest.java

@@ -0,0 +1,141 @@
+package org.brapi.test.BrAPITestServer.model.dto.geno;
+
+import java.util.List;
+
+public class VariantWriteRequest {
+    private String variantDbId;
+    private String variantName;
+    private String variantType;
+    private String variantSetDbId;
+    private String referenceSetDbId;
+    private Integer start;
+    private Integer end;
+    private String referenceBases;
+    private Integer svlen;
+    private Boolean filtersApplied;
+    private Boolean filtersPassed;
+    private List<String> alternateBases;
+    private List<Integer> ciend;
+    private List<Integer> cipos;
+    private List<String> filtersFailed;
+
+    public String getVariantDbId() {
+        return variantDbId;
+    }
+
+    public void setVariantDbId(String variantDbId) {
+        this.variantDbId = variantDbId;
+    }
+
+    public String getVariantName() {
+        return variantName;
+    }
+
+    public void setVariantName(String variantName) {
+        this.variantName = variantName;
+    }
+
+    public String getVariantType() {
+        return variantType;
+    }
+
+    public void setVariantType(String variantType) {
+        this.variantType = variantType;
+    }
+
+    public String getVariantSetDbId() {
+        return variantSetDbId;
+    }
+
+    public void setVariantSetDbId(String variantSetDbId) {
+        this.variantSetDbId = variantSetDbId;
+    }
+
+    public String getReferenceSetDbId() {
+        return referenceSetDbId;
+    }
+
+    public void setReferenceSetDbId(String referenceSetDbId) {
+        this.referenceSetDbId = referenceSetDbId;
+    }
+
+    public Integer getStart() {
+        return start;
+    }
+
+    public void setStart(Integer start) {
+        this.start = start;
+    }
+
+    public Integer getEnd() {
+        return end;
+    }
+
+    public void setEnd(Integer end) {
+        this.end = end;
+    }
+
+    public String getReferenceBases() {
+        return referenceBases;
+    }
+
+    public void setReferenceBases(String referenceBases) {
+        this.referenceBases = referenceBases;
+    }
+
+    public Integer getSvlen() {
+        return svlen;
+    }
+
+    public void setSvlen(Integer svlen) {
+        this.svlen = svlen;
+    }
+
+    public Boolean getFiltersApplied() {
+        return filtersApplied;
+    }
+
+    public void setFiltersApplied(Boolean filtersApplied) {
+        this.filtersApplied = filtersApplied;
+    }
+
+    public Boolean getFiltersPassed() {
+        return filtersPassed;
+    }
+
+    public void setFiltersPassed(Boolean filtersPassed) {
+        this.filtersPassed = filtersPassed;
+    }
+
+    public List<String> getAlternateBases() {
+        return alternateBases;
+    }
+
+    public void setAlternateBases(List<String> alternateBases) {
+        this.alternateBases = alternateBases;
+    }
+
+    public List<Integer> getCiend() {
+        return ciend;
+    }
+
+    public void setCiend(List<Integer> ciend) {
+        this.ciend = ciend;
+    }
+
+    public List<Integer> getCipos() {
+        return cipos;
+    }
+
+    public void setCipos(List<Integer> cipos) {
+        this.cipos = cipos;
+    }
+
+    public List<String> getFiltersFailed() {
+        return filtersFailed;
+    }
+
+    public void setFiltersFailed(List<String> filtersFailed) {
+        this.filtersFailed = filtersFailed;
+    }
+}

src/main/java/org/brapi/test/BrAPITestServer/repository/geno/CallSetRepository.java

@@ -1,7 +1,19 @@
 package org.brapi.test.BrAPITestServer.repository.geno;
 
+import java.util.Collection;
+import java.util.List;
+
 import org.brapi.test.BrAPITestServer.model.entity.geno.CallSetEntity;
 import org.brapi.test.BrAPITestServer.repository.BrAPIRepository;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
+
+public interface CallSetRepository extends BrAPIRepository<CallSetEntity, String> {
+
+	@Query("SELECT COUNT(cs) FROM CallSetEntity cs JOIN cs.variantSets vs WHERE vs.id = :variantSetDbId")
+	long countByVariantSetDbId(@Param("variantSetDbId") String variantSetDbId);
+
+	@Query("SELECT vs.id, COUNT(cs) FROM CallSetEntity cs JOIN cs.variantSets vs WHERE vs.id IN :variantSetDbIds GROUP BY vs.id")
+	List<Object[]> countCallSetsGroupedByVariantSetId(@Param("variantSetDbIds") Collection<String> variantSetDbIds);
 
-public interface CallSetRepository extends BrAPIRepository<CallSetEntity, String>{
 }

src/main/java/org/brapi/test/BrAPITestServer/repository/geno/VariantRepository.java

@@ -1,8 +1,18 @@
 package org.brapi.test.BrAPITestServer.repository.geno;
 
+import java.util.Collection;
+import java.util.List;
+
 import org.brapi.test.BrAPITestServer.model.entity.geno.VariantEntity;
 import org.brapi.test.BrAPITestServer.repository.BrAPIRepository;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
 
 public interface VariantRepository extends BrAPIRepository<VariantEntity, String> {
 
+	long countByVariantSet_Id(String variantSetId);
+
+	@Query("SELECT v.variantSet.id, COUNT(v) FROM VariantEntity v WHERE v.variantSet.id IN :variantSetDbIds GROUP BY v.variantSet.id")
+	List<Object[]> countVariantsGroupedByVariantSetId(@Param("variantSetDbIds") Collection<String> variantSetDbIds);
+
 }

src/main/java/org/brapi/test/BrAPITestServer/service/geno/VariantService.java

@@ -1,18 +1,29 @@
 package org.brapi.test.BrAPITestServer.service.geno;
 
 import java.util.Arrays;
+import java.util.Date;
 import java.util.List;
 import java.util.Optional;
 import java.util.stream.Collectors;
 
 import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerDbIdNotFoundException;
 import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerException;
+import org.brapi.test.BrAPITestServer.model.dto.geno.VariantWriteRequest;
+import org.brapi.test.BrAPITestServer.model.entity.geno.CallEntity;
+import org.brapi.test.BrAPITestServer.model.entity.geno.MarkerPositionEntity;
+import org.brapi.test.BrAPITestServer.model.entity.geno.ReferenceSetEntity;
 import org.brapi.test.BrAPITestServer.model.entity.geno.VariantEntity;
+import org.brapi.test.BrAPITestServer.model.entity.geno.VariantSetEntity;
+import org.brapi.test.BrAPITestServer.repository.geno.CallRepository;
+import org.brapi.test.BrAPITestServer.repository.geno.MarkerPositionRepository;
 import org.brapi.test.BrAPITestServer.repository.geno.VariantRepository;
+import org.brapi.test.BrAPITestServer.repository.geno.VariantSetRepository;
 import org.brapi.test.BrAPITestServer.service.DateUtility;
 import org.brapi.test.BrAPITestServer.service.PagingUtility;
 import org.brapi.test.BrAPITestServer.service.SearchQueryBuilder;
+import org.springframework.dao.DataIntegrityViolationException;
 import org.springframework.data.domain.Page;
+import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Pageable;
 import org.springframework.http.HttpStatus;
 import org.springframework.stereotype.Service;
@@ -25,9 +36,19 @@ import io.swagger.model.geno.VariantsSearchRequest;
 public class VariantService {
 
 	private final VariantRepository variantRepository;
+	private final CallRepository callRepository;
+	private final MarkerPositionRepository markerPositionRepository;
+	private final VariantSetRepository variantSetRepository;
+	private final ReferenceSetService referenceSetService;
 
-	public VariantService(VariantRepository variantRepository) {
+	public VariantService(VariantRepository variantRepository, CallRepository callRepository,
+			MarkerPositionRepository markerPositionRepository, VariantSetRepository variantSetRepository,
+			ReferenceSetService referenceSetService) {
 		this.variantRepository = variantRepository;
+		this.callRepository = callRepository;
+		this.markerPositionRepository = markerPositionRepository;
+		this.variantSetRepository = variantSetRepository;
+		this.referenceSetService = referenceSetService;
 	}
 
 	public List<Variant> findVariants(String variantDbId, String variantSetDbId, String referenceDbId,
@@ -61,7 +82,8 @@ public class VariantService {
 					"*callSet.id");
 		}
 		searchQuery = searchQuery.appendList(request.getVariantSetDbIds(), "variantSet.id")
-				.appendList(request.getVariantDbIds(), "id");
+				.appendList(request.getVariantDbIds(), "id")
+				.appendList(request.getReferenceSetDbIds(), "referenceSet.id");
 
 		Page<VariantEntity> page = variantRepository.findAllBySearch(searchQuery, pageReq);
 		PagingUtility.calculateMetaData(metadata, page);
@@ -99,14 +121,19 @@ public class VariantService {
 		variant.setFiltersFailed(entity.getFiltersFailed());
 		variant.setFiltersPassed(entity.getFiltersPassed());
 		variant.setReferenceBases(entity.getReferenceBases());
-		if (entity.getReferenceSet() != null)
+		if (entity.getReferenceSet() != null) {
+			variant.setReferenceSetDbId(entity.getReferenceSet().getId());
+			variant.setReferenceSetName(entity.getReferenceSet().getReferenceSetName());
 			variant.setReferenceName(entity.getReferenceSet().getReferenceSetName());
+		}
 		variant.setStart(entity.getStart());
 		variant.setSvlen(entity.getSvlen());
 		variant.setUpdated(DateUtility.toOffsetDateTime(entity.getUpdated()));
 		variant.setVariantDbId(entity.getId());
 		variant.setVariantNames(Arrays.asList(entity.getVariantName()));
-		variant.setVariantSetDbId(Arrays.asList(entity.getVariantSet().getId()));
+		if (entity.getVariantSet() != null) {
+			variant.setVariantSetDbId(Arrays.asList(entity.getVariantSet().getId()));
+		}
 		variant.setVariantType(entity.getVariantType());
 
 		return variant;
@@ -116,4 +143,108 @@ public class VariantService {
 		return variantRepository.save(entity);
 	}
 
+	public Variant saveVariant(VariantWriteRequest request) throws BrAPIServerException {
+		if (request.getVariantName() == null || request.getVariantName().isBlank()) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "variantName is required");
+		}
+		if (request.getVariantDbId() != null && variantRepository.findById(request.getVariantDbId()).isPresent()) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT, "Variant already exists: " + request.getVariantDbId());
+		}
+		VariantEntity entity = new VariantEntity();
+		if (request.getVariantDbId() != null && !request.getVariantDbId().isBlank()) {
+			entity.setId(request.getVariantDbId().trim());
+		}
+		entity.setCreated(new Date());
+		entity.setUpdated(new Date());
+		updateEntity(entity, request);
+		return convertFromEntity(variantRepository.save(entity));
+	}
+
+	public Variant updateVariant(String variantDbId, VariantWriteRequest request) throws BrAPIServerException {
+		VariantEntity entity = getVariantEntity(variantDbId, HttpStatus.NOT_FOUND);
+		entity.setUpdated(new Date());
+		updateEntity(entity, request);
+		return convertFromEntity(variantRepository.save(entity));
+	}
+
+	public Variant deleteVariant(String variantDbId) throws BrAPIServerException {
+		VariantEntity entity = getVariantEntity(variantDbId, HttpStatus.NOT_FOUND);
+		assertNoVariantDependencies(variantDbId);
+		Variant deleted = convertFromEntity(entity);
+		try {
+			variantRepository.delete(entity);
+			variantRepository.flush();
+		} catch (DataIntegrityViolationException e) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT, "Variant is in use and cannot be deleted");
+		}
+		return deleted;
+	}
+
+	private void assertNoVariantDependencies(String variantDbId) throws BrAPIServerException {
+		Pageable pageReq = PageRequest.of(0, 1);
+		SearchQueryBuilder<CallEntity> callQuery = new SearchQueryBuilder<CallEntity>(CallEntity.class)
+				.appendSingle(variantDbId, "variant.id");
+		if (callRepository.findAllBySearch(callQuery, pageReq).getTotalElements() > 0) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT, "Variant is referenced by allele_call records");
+		}
+		SearchQueryBuilder<MarkerPositionEntity> markerQuery = new SearchQueryBuilder<MarkerPositionEntity>(
+				MarkerPositionEntity.class).appendSingle(variantDbId, "variant.id");
+		if (markerPositionRepository.findAllBySearch(markerQuery, pageReq).getTotalElements() > 0) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT, "Variant is referenced by marker_position records");
+		}
+	}
+
+	private void updateEntity(VariantEntity entity, VariantWriteRequest request) throws BrAPIServerException {
+		entity.setVariantName(request.getVariantName().trim());
+		entity.setVariantType(request.getVariantType());
+		entity.setStart(request.getStart());
+		entity.setEnd(request.getEnd());
+		if (request.getStart() != null && request.getEnd() != null && request.getEnd() < request.getStart()) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "variant end cannot be less than start");
+		}
+		entity.setReferenceBases(request.getReferenceBases());
+		entity.setSvlen(request.getSvlen());
+		entity.setFiltersApplied(request.getFiltersApplied());
+		entity.setFiltersPassed(request.getFiltersPassed());
+		if (request.getAlternateBases() != null) {
+			entity.setAlternateBases(request.getAlternateBases());
+		}
+		if (request.getCiend() != null) {
+			entity.setCiend(request.getCiend());
+		}
+		if (request.getCipos() != null) {
+			entity.setCipos(request.getCipos());
+		}
+		if (request.getFiltersFailed() != null) {
+			entity.setFiltersFailed(request.getFiltersFailed());
+		}
+
+		VariantSetEntity variantSet = null;
+		if (request.getVariantSetDbId() != null && !request.getVariantSetDbId().isBlank()) {
+			variantSet = variantSetRepository.findById(request.getVariantSetDbId())
+					.orElseThrow(() -> new BrAPIServerDbIdNotFoundException("variantSet", request.getVariantSetDbId(),
+							HttpStatus.BAD_REQUEST));
+			entity.setVariantSet(variantSet);
+		} else if (request.getVariantSetDbId() != null) {
+			entity.setVariantSet(null);
+		}
+
+		ReferenceSetEntity referenceSet = null;
+		if (request.getReferenceSetDbId() != null && !request.getReferenceSetDbId().isBlank()) {
+			referenceSet = referenceSetService.getReferenceSetEntity(request.getReferenceSetDbId());
+			entity.setReferenceSet(referenceSet);
+		} else if (request.getReferenceSetDbId() != null) {
+			entity.setReferenceSet(null);
+		} else if (variantSet != null && variantSet.getReferenceSet() != null) {
+			entity.setReferenceSet(variantSet.getReferenceSet());
+		}
+
+		if (variantSet != null && referenceSet != null
+				&& variantSet.getReferenceSet() != null
+				&& !variantSet.getReferenceSet().getId().equals(referenceSet.getId())) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST,
+					"referenceSetDbId must match the reference set of the selected variantSet");
+		}
+	}
+
 }

src/main/java/org/brapi/test/BrAPITestServer/service/geno/VariantSetService.java

@@ -9,17 +9,24 @@ import java.util.stream.Collectors;
 
 import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerDbIdNotFoundException;
 import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerException;
+import org.brapi.test.BrAPITestServer.model.dto.geno.VariantSetWriteRequest;
+import org.brapi.test.BrAPITestServer.model.entity.core.StudyEntity;
 import org.brapi.test.BrAPITestServer.model.entity.geno.CallEntity;
+import org.brapi.test.BrAPITestServer.model.entity.geno.ReferenceSetEntity;
 import org.brapi.test.BrAPITestServer.model.entity.geno.CallSetEntity;
 import org.brapi.test.BrAPITestServer.model.entity.geno.VariantEntity;
 import org.brapi.test.BrAPITestServer.model.entity.geno.VariantSetAnalysisEntity;
 import org.brapi.test.BrAPITestServer.model.entity.geno.VariantSetAvailableFormatEntity;
 import org.brapi.test.BrAPITestServer.model.entity.geno.VariantSetEntity;
+import org.brapi.test.BrAPITestServer.repository.geno.CallSetRepository;
+import org.brapi.test.BrAPITestServer.repository.geno.VariantRepository;
 import org.brapi.test.BrAPITestServer.repository.geno.VariantSetRepository;
+import org.brapi.test.BrAPITestServer.service.core.StudyService;
 import org.brapi.test.BrAPITestServer.service.DateUtility;
 import org.brapi.test.BrAPITestServer.service.PagingUtility;
 import org.brapi.test.BrAPITestServer.service.SearchQueryBuilder;
 import org.brapi.test.BrAPITestServer.service.UpdateUtility;
+import org.springframework.dao.DataIntegrityViolationException;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 import org.springframework.http.HttpStatus;
@@ -41,16 +48,25 @@ import io.swagger.model.geno.VariantSetsExtractRequest;
 public class VariantSetService {
 
 	private final VariantSetRepository variantSetRepository;
+	private final VariantRepository variantRepository;
+	private final CallSetRepository callSetRepository;
 	private final VariantService variantService;
 	private final CallSetService callSetService;
 	private final CallService callService;
+	private final ReferenceSetService referenceSetService;
+	private final StudyService studyService;
 
-	public VariantSetService(VariantSetRepository variantSetRepository, VariantService variantService,
+	public VariantSetService(VariantSetRepository variantSetRepository, VariantRepository variantRepository,
-			CallSetService callSetService, CallService callService) {
+			CallSetRepository callSetRepository, VariantService variantService, CallSetService callSetService,
+			CallService callService, ReferenceSetService referenceSetService, StudyService studyService) {
 		this.variantSetRepository = variantSetRepository;
+		this.variantRepository = variantRepository;
+		this.callSetRepository = callSetRepository;
 		this.variantService = variantService;
 		this.callSetService = callSetService;
 		this.callService = callService;
+		this.referenceSetService = referenceSetService;
+		this.studyService = studyService;
 	}
 
 	public List<VariantSet> findVariantSets(String variantSetDbId, String variantDbId, String callSetDbId,
@@ -79,9 +95,7 @@ public class VariantSetService {
 	}
 
 	public List<VariantSet> findVariantSets(VariantSetsSearchRequest request, Metadata metadata) {
-		List<VariantSet> variantSets = findVariantSetEntities(request, metadata).stream().map(this::convertFromEntity)
+		return convertFromEntities(findVariantSetEntities(request, metadata));
-				.collect(Collectors.toList());
-		return variantSets;
 	}
 
 	private List<VariantSetEntity> findVariantSetEntities(VariantSetsSearchRequest request, Metadata metadata) {
@@ -95,7 +109,9 @@ public class VariantSetService {
 			searchQuery.join("variants", "variant").appendList(request.getVariantDbIds(), "*variant.id");
 		}
 		searchQuery.appendList(request.getStudyDbIds(), "study.id")
-				.appendList(request.getStudyNames(), "study.studyName").appendList(request.getVariantSetDbIds(), "id");
+				.appendList(request.getStudyNames(), "study.studyName")
+				.appendList(request.getReferenceSetDbIds(), "referenceSet.id")
+				.appendList(request.getVariantSetDbIds(), "id");
 
 		Page<VariantSetEntity> page = variantSetRepository.findAllBySearch(searchQuery, pageReq);
 		PagingUtility.calculateMetaData(metadata, page);
@@ -106,6 +122,74 @@ public class VariantSetService {
 		return convertFromEntity(getVariantSetEntity(variantSetDbId, HttpStatus.NOT_FOUND));
 	}
 
+	public VariantSet saveVariantSet(VariantSetWriteRequest request) throws BrAPIServerException {
+		if (request.getVariantSetName() == null || request.getVariantSetName().isBlank()) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "variantSetName is required");
+		}
+		if (request.getVariantSetDbId() != null
+				&& variantSetRepository.findById(request.getVariantSetDbId()).isPresent()) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT,
+					"VariantSet already exists: " + request.getVariantSetDbId());
+		}
+		VariantSetEntity entity = new VariantSetEntity();
+		if (request.getVariantSetDbId() != null && !request.getVariantSetDbId().isBlank()) {
+			entity.setId(request.getVariantSetDbId().trim());
+		}
+		updateEntity(entity, request);
+		return convertFromEntity(variantSetRepository.save(entity));
+	}
+
+	public VariantSet updateVariantSet(String variantSetDbId, VariantSetWriteRequest request)
+			throws BrAPIServerException {
+		VariantSetEntity entity = getVariantSetEntity(variantSetDbId, HttpStatus.NOT_FOUND);
+		updateEntity(entity, request);
+		return convertFromEntity(variantSetRepository.save(entity));
+	}
+
+	public VariantSet deleteVariantSet(String variantSetDbId) throws BrAPIServerException {
+		VariantSetEntity entity = getVariantSetEntity(variantSetDbId, HttpStatus.NOT_FOUND);
+		assertNoVariantSetDependencies(entity);
+		VariantSet deleted = convertFromEntity(entity);
+		try {
+			variantSetRepository.delete(entity);
+			variantSetRepository.flush();
+		} catch (DataIntegrityViolationException e) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT, "VariantSet is in use and cannot be deleted");
+		}
+		return deleted;
+	}
+
+	private void assertNoVariantSetDependencies(VariantSetEntity entity) throws BrAPIServerException {
+		if (entity.getVariants() != null && !entity.getVariants().isEmpty()) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT, "VariantSet is referenced by Variant records");
+		}
+		if (entity.getCallSets() != null && !entity.getCallSets().isEmpty()) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT, "VariantSet is referenced by CallSet records");
+		}
+		if (entity.getAnalysis() != null && !entity.getAnalysis().isEmpty()) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT, "VariantSet is referenced by analysis records");
+		}
+		if (entity.getAvailableFormats() != null && !entity.getAvailableFormats().isEmpty()) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT, "VariantSet is referenced by available format records");
+		}
+	}
+
+	private void updateEntity(VariantSetEntity entity, VariantSetWriteRequest request) throws BrAPIServerException {
+		entity.setVariantSetName(request.getVariantSetName().trim());
+		if (request.getReferenceSetDbId() != null && !request.getReferenceSetDbId().isBlank()) {
+			ReferenceSetEntity referenceSet = referenceSetService.getReferenceSetEntity(request.getReferenceSetDbId());
+			entity.setReferenceSet(referenceSet);
+		} else if (request.getReferenceSetDbId() != null) {
+			entity.setReferenceSet(null);
+		}
+		if (request.getStudyDbId() != null && !request.getStudyDbId().isBlank()) {
+			StudyEntity study = studyService.getStudyEntity(request.getStudyDbId());
+			entity.setStudy(study);
+		} else if (request.getStudyDbId() != null) {
+			entity.setStudy(null);
+		}
+	}
+
 	public VariantSetEntity getVariantSetEntity(String variantSetDbId) throws BrAPIServerException {
 		return getVariantSetEntity(variantSetDbId, HttpStatus.BAD_REQUEST);
 	}
@@ -122,7 +206,34 @@ public class VariantSetService {
 		return variantSet;
 	}
 
+	private List<VariantSet> convertFromEntities(List<VariantSetEntity> entities) {
+		if (entities.isEmpty()) {
+			return List.of();
+		}
+		List<String> variantSetDbIds = entities.stream().map(VariantSetEntity::getId).collect(Collectors.toList());
+		Map<String, Long> variantCounts = toCountMap(variantRepository.countVariantsGroupedByVariantSetId(variantSetDbIds));
+		Map<String, Long> callSetCounts = toCountMap(callSetRepository.countCallSetsGroupedByVariantSetId(variantSetDbIds));
+		return entities.stream()
+				.map(entity -> convertFromEntity(entity,
+						variantCounts.getOrDefault(entity.getId(), 0L),
+						callSetCounts.getOrDefault(entity.getId(), 0L)))
+				.collect(Collectors.toList());
+	}
+
+	private Map<String, Long> toCountMap(List<Object[]> rows) {
+		Map<String, Long> counts = new HashMap<>();
+		for (Object[] row : rows) {
+			counts.put((String) row[0], ((Number) row[1]).longValue());
+		}
+		return counts;
+	}
+
 	private VariantSet convertFromEntity(VariantSetEntity entity) {
+		return convertFromEntity(entity, variantRepository.countByVariantSet_Id(entity.getId()),
+				callSetRepository.countByVariantSetDbId(entity.getId()));
+	}
+
+	private VariantSet convertFromEntity(VariantSetEntity entity, long variantCount, long callSetCount) {
 		VariantSet variantSet = new VariantSet();
 		UpdateUtility.convertFromEntity(entity, variantSet);
 		if (entity.getAnalysis() != null)
@@ -131,14 +242,12 @@ public class VariantSetService {
 		if (entity.getAvailableFormats() != null)
 			variantSet.setAvailableFormats(
 					entity.getAvailableFormats().stream().map(this::convertFromEntity).collect(Collectors.toList()));
-		if (entity.getCallSets() != null)
+		variantSet.setCallSetCount(toCountInteger(callSetCount));
-			variantSet.setCallSetCount(entity.getCallSets().size());
 		if (entity.getReferenceSet() != null)
 			variantSet.setReferenceSetDbId(entity.getReferenceSet().getId());
 		if (entity.getStudy() != null)
 			variantSet.setStudyDbId(entity.getStudy().getId());
-		if (entity.getVariants() != null)
+		variantSet.setVariantCount(toCountInteger(variantCount));
-			variantSet.setVariantCount(entity.getVariants().size());
 		variantSet.setVariantSetDbId(entity.getId());
 		variantSet.setVariantSetName(entity.getVariantSetName());
 
@@ -163,6 +272,10 @@ public class VariantSetService {
 		return variantSet;
 	}
 
+	private Integer toCountInteger(long count) {
+		return count > Integer.MAX_VALUE ? Integer.MAX_VALUE : (int) count;
+	}
+
 	private Analysis convertFromEntity(VariantSetAnalysisEntity entity) {
 		Analysis analysis = new Analysis();
 		analysis.setAnalysisDbId(entity.getId());