fix:第三章开发结束

AGENTS.md

@@ -3,3 +3,14 @@
 3.下拉框的数据要缓存下来，同一选项源不要重复请求接口。
 4.前端首页（及同类入口页）加载首页数据时，副作用只触发一次查询，避免 Strict Mode 或重复 mount 导致多次请求。
 5.保存、提交类操作要做防抖（debounce），防止连续点击重复提交。
+6.每完成一份 `docs/dev/**` 下的开发文档对应功能（页面、接口、校验等与文档要求一致）后，在该文档末尾追加完成标注，格式如下：
+
+```markdown
+---
+
+**状态：已完成**
+```
+
+- 仅在该文档描述的功能全部落地时标注；部分实现（如仅后端、缺页面或缺校验）不要标注。
+- 若文档末尾已有「状态：已完成」，不要重复追加。
+- `docs/dev/**/README.md` 等索引/说明类文档无需标注。

docs/dev/03-genotyping/08-callset.md

@@ -38,3 +38,7 @@
 1. `sample_id` 必须存在。
 2. 删除 callset 前检查 `allele_call` 和 `callset_variant_sets`。
 3. 如果 callset 绑定多个 variantset，查询和导出时要明确当前 variantset 范围。
+
+---
+
+**状态：已完成**

docs/dev/03-genotyping/12-marker_position.md

@@ -37,3 +37,7 @@
 1. `linkage_group_id` 和 `variant_id` 必须存在。
 2. 同一 linkage group 下同一 variant 不应重复。
 3. `position` 不应超过 linkage group 的 `max_marker_position`。
+
+---
+
+**状态：已完成**

docs/dev/03-genotyping/13-callset_variant_sets.md

@@ -32,3 +32,7 @@
 1. `call_sets_id` 和 `variant_sets_id` 必须存在。
 2. 同一 callset 与 variantset 关系不应重复。
 3. 删除关系不应删除 callset 或 variantset 主数据。
+
+---
+
+**状态：已完成**

docs/dev/03-genotyping/14-variantset_analysis.md

@@ -43,3 +43,7 @@
 1. `variant_set_id` 必须存在。
 2. 删除 variantset 时需要先处理或级联处理 analysis。
 3. `software` 如果是 URL，前端可做 URL 格式提示。
+
+---
+
+**状态：已完成**

docs/dev/03-genotyping/15-variantset_format.md

@@ -40,3 +40,7 @@
 1. `variant_set_id` 必须存在。
 2. `fileurl` 如填写需通过 URL 格式校验。
 3. 对矩阵格式，`sep_phased/sep_unphased/unknown_string` 会影响解析，应在导入预览时展示。
+
+---
+
+**状态：已完成**

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

@@ -0,0 +1,318 @@
+import { createCachedLoader } from "@/services/dropdownCache";
+import { getAuthToken } from "@/utils/token";
+import {
+  NONE_SELECT_VALUE,
+  type AlleleCallQuery,
+  type AlleleCallRecord,
+  type CallSetDetail,
+  type CallSetQuery,
+  type CallSetRecord,
+  type SelectOption,
+} 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 SampleResponse {
+  sampleDbId: string;
+  sampleName: string | null;
+}
+
+interface VariantSetLookup {
+  value: string;
+  label: string;
+}
+
+type CallSetPayload = Partial<Record<
+  "id" | "call_set_name" | "sample_id" | "variant_set_ids",
+  unknown
+>>;
+
+type AlleleCallPayload = Partial<Record<
+  "call_set_id" | "variant_id" | "genotype" | "read_depth" | "phase_set",
+  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 normalizeVariantSetIds = (value: unknown): string[] => {
+  if (!Array.isArray(value)) return [];
+  return value
+    .map((item) => String(item ?? "").trim())
+    .filter(Boolean);
+};
+
+const sampleLoader = createCachedLoader(async () => {
+  const response = await request<BrapiListResponse<SampleResponse>>("/brapi/v2/samples?page=0&pageSize=10");
+  return response.result.data.map((item) => ({
+    value: item.sampleDbId,
+    label: item.sampleName || item.sampleDbId,
+  }));
+});
+
+const variantSetLoader = createCachedLoader(async () => {
+  const response = await request<BrapiListResponse<{ variantSetDbId: string; variantSetName: string | null }>>(
+    "/brapi/v2/variantsets?page=0&pageSize=10",
+  );
+  return response.result.data.map((item) => ({
+    value: item.variantSetDbId,
+    label: item.variantSetName || item.variantSetDbId,
+  }));
+});
+
+export function invalidateCallSetPageCache() {
+  sampleLoader.invalidate();
+  variantSetLoader.invalidate();
+}
+
+const mapCallSet = (
+  item: CallSetRecord,
+  samples: SelectOption[],
+  variantSets: VariantSetLookup[],
+): CallSetRecord => {
+  const sampleDbId = item.sampleDbId || item.sample_id || null;
+  const sample = samples.find((entry) => entry.value === sampleDbId);
+  const variantSetIds = normalizeVariantSetIds(item.variantSetDbIds ?? item.variant_set_ids);
+  const variantSetNames = variantSetIds
+    .map((id) => variantSets.find((entry) => entry.value === id)?.label || id)
+    .join("、");
+
+  return {
+    ...item,
+    id: item.callSetDbId || item.id,
+    call_set_name: item.call_set_name || item.callSetName || null,
+    sample_id: sampleDbId,
+    sample_name: item.sample_name || item.sampleName || sample?.label || null,
+    variant_set_ids: variantSetIds,
+    variant_set_names: variantSetNames || "—",
+  };
+};
+
+const filterCallSetRows = (
+  rows: CallSetRecord[],
+  query: CallSetQuery | undefined,
+  samples: SelectOption[],
+  variantSets: VariantSetLookup[],
+): CallSetRecord[] => {
+  const nameFilter = String(query?.call_set_name ?? "").trim().toLowerCase();
+  const sampleId = optionalText(query?.sample_id);
+  const variantSetId = optionalText(query?.variant_set_id);
+
+  return rows
+    .map((item) => mapCallSet(item, samples, variantSets))
+    .filter((item) => {
+      if (nameFilter && !String(item.call_set_name ?? "").toLowerCase().includes(nameFilter)) return false;
+      if (sampleId && item.sample_id !== sampleId) return false;
+      if (variantSetId && !(item.variant_set_ids ?? []).includes(variantSetId)) return false;
+      return true;
+    });
+};
+
+const callSetBody = (payload: CallSetPayload) => ({
+  callSetName: requiredText(payload.call_set_name, "CallSet 名称不能为空"),
+  sampleDbId: requiredText(payload.sample_id, "Sample 不能为空"),
+  variantSetDbIds: normalizeVariantSetIds(payload.variant_set_ids),
+});
+
+export const normalizeCallSetFormData = (row: CallSetRecord) => ({
+  id: row.id,
+  call_set_name: row.call_set_name || row.callSetName || "",
+  sample_id: row.sample_id && row.sample_id !== NONE_SELECT_VALUE ? row.sample_id : NONE_SELECT_VALUE,
+  variant_set_ids: normalizeVariantSetIds(row.variant_set_ids ?? row.variantSetDbIds),
+});
+
+export async function loadCallSetPageData(params: {
+  query?: CallSetQuery;
+  force?: boolean;
+} = {}): Promise<{
+  options: { samples: SelectOption[]; variantSets: SelectOption[] };
+  rows: CallSetRecord[];
+}> {
+  const force = params.force ?? false;
+  const [samples, variantSets] = await Promise.all([
+    sampleLoader.load(force),
+    variantSetLoader.load(force),
+  ]);
+
+  const searchParams = new URLSearchParams({ page: "0", pageSize: "10" });
+  const sampleId = optionalText(params.query?.sample_id);
+  const variantSetId = optionalText(params.query?.variant_set_id);
+  if (sampleId) searchParams.set("sampleDbId", sampleId);
+  if (variantSetId) searchParams.set("variantSetDbId", variantSetId);
+
+  const response = await request<BrapiListResponse<CallSetRecord>>(
+    `/brapi/v2/callsets?${searchParams.toString()}`,
+  );
+
+  return {
+    options: { samples, variantSets },
+    rows: filterCallSetRows(response.result.data, params.query, samples, variantSets),
+  };
+}
+
+export async function fetchCallSetDetail(callSetDbId: string): Promise<CallSetDetail> {
+  const [detail, samples, variantSets] = await Promise.all([
+    request<BrapiSingleResponse<CallSetRecord>>(`/brapi/v2/callsets/${encodeURIComponent(callSetDbId)}`),
+    sampleLoader.load(),
+    variantSetLoader.load(),
+  ]);
+  return mapCallSet(detail.result, samples, variantSets) as CallSetDetail;
+}
+
+export async function createCallSetRow(payload: CallSetPayload): Promise<CallSetRecord> {
+  const response = await request<BrapiListResponse<CallSetRecord>>("/brapi/v2/callsets", {
+    method: "POST",
+    body: JSON.stringify({
+      callSetDbId: optionalText(payload.id),
+      ...callSetBody(payload),
+    }),
+  });
+  invalidateCallSetPageCache();
+  const [samples, variantSets] = await Promise.all([
+    sampleLoader.load(true),
+    variantSetLoader.load(true),
+  ]);
+  return mapCallSet(response.result.data[0], samples, variantSets);
+}
+
+export async function updateCallSetRow(id: string, payload: CallSetPayload): Promise<CallSetRecord> {
+  const requestedId = optionalText(payload.id);
+  if (requestedId && requestedId !== id) {
+    throw new Error("CallSet ID 不可修改，请新建记录");
+  }
+  const response = await request<BrapiSingleResponse<CallSetRecord>>(
+    `/brapi/v2/callsets/${encodeURIComponent(id)}`,
+    {
+      method: "PUT",
+      body: JSON.stringify(callSetBody(payload)),
+    },
+  );
+  invalidateCallSetPageCache();
+  const [samples, variantSets] = await Promise.all([
+    sampleLoader.load(true),
+    variantSetLoader.load(true),
+  ]);
+  return mapCallSet(response.result, samples, variantSets);
+}
+
+export async function deleteCallSetRow(id: string): Promise<void> {
+  await request(`/brapi/v2/callsets/${encodeURIComponent(id)}`, { method: "DELETE" });
+  invalidateCallSetPageCache();
+}
+
+const mapAlleleCall = (item: AlleleCallRecord & { additionalInfo?: Record<string, unknown> }): AlleleCallRecord => ({
+  ...item,
+  id: String(item.additionalInfo?.callDbId ?? item.callDbId ?? item.id ?? ""),
+  call_set_id: item.callSetDbId || item.call_set_id || null,
+  call_set_name: item.callSetName || item.call_set_name || null,
+  variant_id: item.variantDbId || item.variant_id || null,
+  variant_name: item.variantName || item.variant_name || null,
+  variant_set_id: item.variantSetDbId || item.variant_set_id || null,
+  genotype: item.genotypeValue || item.genotype || null,
+});
+
+const filterAlleleCallRows = (rows: AlleleCallRecord[], query?: AlleleCallQuery) => {
+  const callSetId = optionalText(query?.call_set_id);
+  const variantId = optionalText(query?.variant_id);
+  const variantSetId = optionalText(query?.variant_set_id);
+
+  return rows
+    .map(mapAlleleCall)
+    .filter((item) => {
+      if (callSetId && item.call_set_id !== callSetId) return false;
+      if (variantId && item.variant_id !== variantId) return false;
+      if (variantSetId && item.variant_set_id !== variantSetId) return false;
+      return true;
+    });
+};
+
+export async function loadAlleleCallRows(query?: AlleleCallQuery): Promise<AlleleCallRecord[]> {
+  const searchParams = new URLSearchParams({ pageSize: "10" });
+  const callSetId = optionalText(query?.call_set_id);
+  const variantId = optionalText(query?.variant_id);
+  const variantSetId = optionalText(query?.variant_set_id);
+  if (callSetId) searchParams.set("callSetDbId", callSetId);
+  if (variantId) searchParams.set("variantDbId", variantId);
+  if (variantSetId) searchParams.set("variantSetDbId", variantSetId);
+
+  const response = await request<BrapiListResponse<AlleleCallRecord>>(
+    `/brapi/v2/calls?${searchParams.toString()}`,
+  );
+  return filterAlleleCallRows(response.result.data, query);
+}
+
+export async function importAlleleCallRows(payloads: AlleleCallPayload[]): Promise<AlleleCallRecord[]> {
+  const body = payloads.map((payload) => ({
+    callDbId: optionalText((payload as Record<string, unknown>).id),
+    callSetDbId: requiredText(payload.call_set_id, "CallSet 不能为空"),
+    variantDbId: requiredText(payload.variant_id, "Variant 不能为空"),
+    genotype: requiredText(payload.genotype, "Genotype 不能为空"),
+    readDepth: payload.read_depth === null || payload.read_depth === undefined || payload.read_depth === ""
+      ? null
+      : Number(payload.read_depth),
+    phaseSet: optionalText(payload.phase_set),
+  }));
+
+  const response = await request<BrapiListResponse<AlleleCallRecord>>("/brapi/v2/calls/import", {
+    method: "POST",
+    body: JSON.stringify(body),
+  });
+  return response.result.data.map(mapAlleleCall);
+}

frontend/src/app/(app)/genotyping/call-set/components/AlleleCallTab.tsx

@@ -0,0 +1,182 @@
+"use client";
+
+import { useCallback, useEffect, useMemo, useState } from "react";
+import { useSearchParams } from "next/navigation";
+import { Dna, RotateCcw, Search } from "lucide-react";
+import { Badge } from "@/components/ui/badge";
+import { Button } from "@/components/ui/button";
+import { Label } from "@/components/ui/label";
+import { Select, SelectContent, SelectItem, SelectTrigger, SelectValue } from "@/components/ui/select";
+import { Skeleton } from "@/components/ui/skeleton";
+import { Table, TableBody, TableCell, TableHead, TableHeader, TableRow } from "@/components/ui/table";
+import { loadAlleleCallRows, loadCallSetPageData } from "../api";
+import { NONE_SELECT_VALUE, type AlleleCallQuery, type AlleleCallRecord, type SelectOption } from "../types";
+
+const emptyQuery = (): AlleleCallQuery => ({
+  call_set_id: NONE_SELECT_VALUE,
+  variant_id: NONE_SELECT_VALUE,
+  variant_set_id: NONE_SELECT_VALUE,
+});
+
+export function AlleleCallTab() {
+  const searchParams = useSearchParams();
+  const [callSetOptions, setCallSetOptions] = useState<SelectOption[]>([]);
+  const [variantSetOptions, setVariantSetOptions] = useState<SelectOption[]>([]);
+  const [draftQuery, setDraftQuery] = useState<AlleleCallQuery>(() => ({
+    ...emptyQuery(),
+    variant_id: searchParams.get("variant_id") || NONE_SELECT_VALUE,
+  }));
+  const [appliedQuery, setAppliedQuery] = useState<AlleleCallQuery>(() => ({
+    ...emptyQuery(),
+    variant_id: searchParams.get("variant_id") || NONE_SELECT_VALUE,
+  }));
+  const [rows, setRows] = useState<AlleleCallRecord[]>([]);
+  const [loading, setLoading] = useState(true);
+  const [error, setError] = useState<string | null>(null);
+
+  useEffect(() => {
+    let mounted = true;
+    loadCallSetPageData()
+      .then(({ options, rows: callSetRows }) => {
+        if (!mounted) return;
+        setCallSetOptions(callSetRows.map((item) => ({
+          value: String(item.id ?? item.callSetDbId ?? ""),
+          label: String(item.call_set_name ?? item.callSetName ?? item.id ?? ""),
+        })).filter((item) => item.value));
+        setVariantSetOptions(options.variantSets);
+      })
+      .catch(() => {
+        if (!mounted) return;
+      });
+    return () => { mounted = false; };
+  }, []);
+
+  const loadRows = useCallback(async () => {
+    return loadAlleleCallRows(appliedQuery);
+  }, [appliedQuery]);
+
+  useEffect(() => {
+    let mounted = true;
+    setLoading(true);
+    setError(null);
+    loadRows()
+      .then((data) => {
+        if (!mounted) return;
+        setRows(data);
+      })
+      .catch((event) => {
+        if (!mounted) return;
+        setError(event instanceof Error ? event.message : "加载 allele_call 失败");
+      })
+      .finally(() => {
+        if (mounted) setLoading(false);
+      });
+    return () => { mounted = false; };
+  }, [loadRows]);
+
+  const hint = useMemo(() => {
+    if (appliedQuery.variant_id && appliedQuery.variant_id !== NONE_SELECT_VALUE) {
+      return "按 Variant 过滤查看该位点下的 genotype 调用结果。";
+    }
+    return "allele_call 通常通过 VCF/HapMap/矩阵导入；导入时会自动绑定 callset 与 variantset 关系。";
+  }, [appliedQuery.variant_id]);
+
+  return (
+    <div className="space-y-4">
+      <div className="rounded-xl border border-slate-200 bg-white p-4 dark:border-slate-800 dark:bg-slate-950">
+        <div className="mb-3 flex items-center gap-2">
+          <Dna className="h-4 w-4 text-emerald-500" />
+          <div>
+            <h2 className="text-base font-semibold">allele_call 调用结果</h2>
+            <p className="text-xs text-slate-500">{hint}</p>
+          </div>
+        </div>
+        <div className="grid gap-3 md:grid-cols-3">
+          <div className="space-y-1.5">
+            <Label className="text-xs text-slate-500">CallSet</Label>
+            <Select
+              value={draftQuery.call_set_id ?? NONE_SELECT_VALUE}
+              onValueChange={(value) => setDraftQuery((current) => ({ ...current, call_set_id: value }))}
+            >
+              <SelectTrigger><SelectValue placeholder="全部" /></SelectTrigger>
+              <SelectContent>
+                <SelectItem value={NONE_SELECT_VALUE}>全部</SelectItem>
+                {callSetOptions.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>
+        <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>
+
+      {error ? (
+        <div className="rounded-xl border border-destructive/20 bg-destructive/10 px-4 py-3 text-sm text-destructive">
+          {error}
+        </div>
+      ) : null}
+
+      <div className="rounded-xl border border-slate-200 bg-white dark:border-slate-800 dark:bg-slate-950">
+        {loading ? (
+          <div className="p-4"><Skeleton className="h-64 w-full" /></div>
+        ) : rows.length === 0 ? (
+          <p className="p-6 text-sm text-slate-500">暂无 allele_call 记录。</p>
+        ) : (
+          <Table>
+            <TableHeader>
+              <TableRow>
+                <TableHead>CallSet</TableHead>
+                <TableHead>Variant</TableHead>
+                <TableHead>VariantSet</TableHead>
+                <TableHead>Genotype</TableHead>
+                <TableHead>Read Depth</TableHead>
+              </TableRow>
+            </TableHeader>
+            <TableBody>
+              {rows.map((row) => (
+                <TableRow key={String(row.id || `${row.call_set_id}-${row.variant_id}`)}>
+                  <TableCell>{row.call_set_name || row.call_set_id || "—"}</TableCell>
+                  <TableCell>{row.variant_name || row.variant_id || "—"}</TableCell>
+                  <TableCell>
+                    <Badge variant="outline">{row.variant_set_id || "—"}</Badge>
+                  </TableCell>
+                  <TableCell>{row.genotype || "—"}</TableCell>
+                  <TableCell>{row.read_depth ?? "—"}</TableCell>
+                </TableRow>
+              ))}
+            </TableBody>
+          </Table>
+        )}
+      </div>
+    </div>
+  );
+}

frontend/src/app/(app)/genotyping/call-set/components/CallSetTab.tsx

@@ -0,0 +1,233 @@
+"use client";
+
+import { useCallback, useMemo, useState } from "react";
+import { useSearchParams } from "next/navigation";
+import { Binary, 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 { Checkbox } from "@/components/ui/checkbox";
+import { Input } from "@/components/ui/input";
+import { Label } from "@/components/ui/label";
+import { Select, SelectContent, SelectItem, SelectTrigger, SelectValue } from "@/components/ui/select";
+import {
+  createCallSetRow,
+  deleteCallSetRow,
+  fetchCallSetDetail,
+  loadCallSetPageData,
+  normalizeCallSetFormData,
+  updateCallSetRow,
+} from "../api";
+import { NONE_SELECT_VALUE, type CallSetQuery, type SelectOption } from "../types";
+
+const emptyQuery = (): CallSetQuery => ({
+  call_set_name: "",
+  sample_id: NONE_SELECT_VALUE,
+  variant_set_id: NONE_SELECT_VALUE,
+});
+
+const optionOrNone = (label: string, options: SelectOption[]) => [
+  { value: NONE_SELECT_VALUE, label },
+  ...options,
+];
+
+function normalizeSelectedVariantSetIds(value: unknown): string[] {
+  if (!Array.isArray(value)) return [];
+  return value.map((item) => String(item ?? "").trim()).filter(Boolean);
+}
+
+export function CallSetTab() {
+  const searchParams = useSearchParams();
+  const [sampleOptions, setSampleOptions] = useState<SelectOption[]>([]);
+  const [variantSetOptions, setVariantSetOptions] = useState<SelectOption[]>([]);
+  const [draftQuery, setDraftQuery] = useState<CallSetQuery>(emptyQuery);
+  const [appliedQuery, setAppliedQuery] = useState<CallSetQuery>(emptyQuery);
+
+  const urlDefaultFormValues = useMemo(() => {
+    const sampleId = searchParams.get("sample_id");
+    if (!sampleId) return undefined;
+    return { sample_id: sampleId };
+  }, [searchParams]);
+
+  const loadRows = useCallback(async () => {
+    const { options, rows } = await loadCallSetPageData({ query: appliedQuery });
+    setSampleOptions(options.samples);
+    setVariantSetOptions(options.variantSets);
+    return rows as unknown as Record<string, unknown>[];
+  }, [appliedQuery]);
+
+  const fetchRecord = useCallback(async (id: string) => {
+    const detail = await fetchCallSetDetail(id);
+    return normalizeCallSetFormData(detail);
+  }, []);
+
+  const fields = useMemo<BrapiFormField[]>(() => [
+    { key: "id", label: "CallSet ID", type: "text", placeholder: "留空则系统自动生成（导入时可指定）" },
+    {
+      key: "call_set_name",
+      label: "CallSet 名称",
+      type: "text",
+      required: true,
+      placeholder: "如 sample01_variantset1",
+    },
+    {
+      key: "sample_id",
+      label: "Sample",
+      type: "select",
+      required: true,
+      options: optionOrNone("请选择 Sample", sampleOptions),
+    },
+  ], [sampleOptions]);
+
+  const renderFormExtra = useCallback(({ formData, updateFormBatch }: {
+    formData: Record<string, unknown>;
+    updateForm: (key: string, value: string) => void;
+    updateFormBatch: (patch: Record<string, unknown>) => void;
+    editingRow: Record<string, unknown> | null;
+  }) => {
+    const selectedIds = normalizeSelectedVariantSetIds(formData.variant_set_ids);
+
+    const toggleVariantSet = (variantSetId: string, checked: boolean) => {
+      const next = checked
+        ? Array.from(new Set([...selectedIds, variantSetId]))
+        : selectedIds.filter((id) => id !== variantSetId);
+      updateFormBatch({ variant_set_ids: next });
+    };
+
+    return (
+      <>
+        <div className="md:col-span-2 space-y-2">
+          <Label className="text-sm text-slate-700 dark:text-slate-200">VariantSet（可多选）</Label>
+          <div className="max-h-48 space-y-2 overflow-y-auto rounded-lg border border-slate-200 p-3 dark:border-slate-800">
+            {variantSetOptions.length === 0 ? (
+              <p className="text-sm text-slate-500">暂无可选 VariantSet，请先在 VariantSet 页面创建。</p>
+            ) : (
+              variantSetOptions.map((option) => {
+                const checked = selectedIds.includes(option.value);
+                return (
+                  <label
+                    key={option.value}
+                    className="flex cursor-pointer items-center gap-2 rounded-md px-1 py-1 text-sm hover:bg-slate-50 dark:hover:bg-slate-900"
+                  >
+                    <Checkbox
+                      checked={checked}
+                      onCheckedChange={(value) => toggleVariantSet(option.value, value === true)}
+                    />
+                    <span>{option.label}</span>
+                  </label>
+                );
+              })
+            )}
+          </div>
+          <p className="text-xs text-slate-500">
+            创建或编辑 CallSet 时绑定 VariantSet；导入 allele_call 时也会自动写入 callset_variant_sets 关系。
+          </p>
+        </div>
+        <div className="col-span-2 rounded-lg border border-sky-100 bg-sky-50/60 p-3 text-xs text-sky-900 dark:border-sky-900/40 dark:bg-sky-950/30 dark:text-sky-100">
+          <p className="font-medium">callset_variant_sets</p>
+          <p className="mt-1 text-sky-800/80 dark:text-sky-200/80">
+            此处勾选会写入 callset 与 variantset 的多对多关系，无需单独维护关系表。
+          </p>
+        </div>
+      </>
+    );
+  }, [variantSetOptions]);
+
+  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">CallSet 名称</Label>
+          <Input
+            value={draftQuery.call_set_name ?? ""}
+            onChange={(event) => setDraftQuery((current) => ({ ...current, call_set_name: event.target.value }))}
+            placeholder="callSetName 模糊匹配"
+          />
+        </div>
+        <div className="space-y-1.5">
+          <Label className="text-xs text-slate-500">Sample</Label>
+          <Select
+            value={draftQuery.sample_id ?? NONE_SELECT_VALUE}
+            onValueChange={(value) => setDraftQuery((current) => ({ ...current, sample_id: value }))}
+          >
+            <SelectTrigger><SelectValue placeholder="全部" /></SelectTrigger>
+            <SelectContent>
+              <SelectItem value={NONE_SELECT_VALUE}>全部</SelectItem>
+              {sampleOptions.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>
+      <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, sampleOptions, variantSetOptions]);
+
+  return (
+    <BrapiEntityPage
+      useEnhancedDialog
+      icon={Binary}
+      iconBg="bg-gradient-to-br from-sky-500 to-blue-600"
+      title="CallSet 调用集合"
+      description="维护 sample 的 genotype call 集合，并绑定其覆盖的 VariantSet。"
+      addLabel="新增 CallSet"
+      defaultFormValues={urlDefaultFormValues}
+      columns={[
+        { key: "call_set_name", label: "名称" },
+        { key: "sample_name", label: "Sample" },
+        {
+          key: "variant_set_names",
+          label: "VariantSet",
+          render: (value) => (
+            <Badge variant="outline" className="max-w-xs truncate">
+              {String(value ?? "—")}
+            </Badge>
+          ),
+        },
+      ]}
+      fields={fields}
+      data={[]}
+      stats={[{
+        label: "/brapi/v2/callsets",
+        value: "BrAPI",
+        className: "bg-sky-50 text-sky-700 dark:bg-sky-400/10 dark:text-sky-200",
+      }]}
+      loadData={loadRows}
+      fetchRecord={fetchRecord}
+      createRecord={(payload) => createCallSetRow(payload) as unknown as Promise<Record<string, unknown>>}
+      updateRecord={(id, payload) => updateCallSetRow(id, payload) as unknown as Promise<Record<string, unknown>>}
+      deleteRecord={deleteCallSetRow}
+      renderQueryForm={renderQueryForm}
+      renderFormExtra={renderFormExtra}
+    />
+  );
+}

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

@@ -0,0 +1,56 @@
+"use client";
+
+import { Suspense, useEffect, useState } from "react";
+import { useSearchParams } from "next/navigation";
+import { Binary, Dna } from "lucide-react";
+import { Tabs, TabsContent, TabsList, TabsTrigger } from "@/components/ui/tabs";
+import { Skeleton } from "@/components/ui/skeleton";
+import { AlleleCallTab } from "./components/AlleleCallTab";
+import { CallSetTab } from "./components/CallSetTab";
+
+function TabFallback() {
+  return <Skeleton className="h-96 w-full rounded-xl" />;
+}
+
+export default function CallSetPage() {
+  const searchParams = useSearchParams();
+  const [tab, setTab] = useState("callsets");
+
+  useEffect(() => {
+    const requested = searchParams.get("tab");
+    if (requested === "allele-calls") {
+      setTab("allele-calls");
+    }
+  }, [searchParams]);
+
+  return (
+    <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="callsets" className="gap-2">
+          <Binary className="h-4 w-4" />
+          CallSet
+        </TabsTrigger>
+        <TabsTrigger value="allele-calls" className="gap-2">
+          <Dna className="h-4 w-4" />
+          allele_call
+        </TabsTrigger>
+      </TabsList>
+
+      {tab === "callsets" ? (
+        <TabsContent value="callsets" className="mt-0 min-h-0 flex-1">
+          <Suspense fallback={<TabFallback />}>
+            <CallSetTab />
+          </Suspense>
+        </TabsContent>
+      ) : null}
+
+      {tab === "allele-calls" ? (
+        <TabsContent value="allele-calls" className="mt-0 min-h-0 flex-1">
+          <Suspense fallback={<TabFallback />}>
+            <AlleleCallTab />
+          </Suspense>
+        </TabsContent>
+      ) : null}
+    </Tabs>
+  );
+}

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

@@ -0,0 +1,57 @@
+export const NONE_SELECT_VALUE = "__none__";
+
+export interface SelectOption {
+  value: string;
+  label: string;
+}
+
+export interface CallSetQuery {
+  call_set_name?: string;
+  sample_id?: string;
+  variant_set_id?: string;
+}
+
+export interface CallSetRecord {
+  id?: string;
+  callSetDbId?: string;
+  call_set_name?: string | null;
+  callSetName?: string | null;
+  sample_id?: string | null;
+  sampleDbId?: string | null;
+  sample_name?: string | null;
+  sampleName?: string | null;
+  variant_set_ids?: string[];
+  variantSetDbIds?: string[] | null;
+  variant_set_names?: string;
+  created?: string | null;
+  updated?: string | null;
+}
+
+export interface CallSetDetail extends CallSetRecord {
+  variant_set_ids: string[];
+}
+
+export interface AlleleCallQuery {
+  call_set_id?: string;
+  variant_id?: string;
+  variant_set_id?: string;
+}
+
+export interface AlleleCallRecord {
+  id?: string;
+  callDbId?: string;
+  call_set_id?: string | null;
+  callSetDbId?: string | null;
+  call_set_name?: string | null;
+  callSetName?: string | null;
+  variant_id?: string | null;
+  variantDbId?: string | null;
+  variant_name?: string | null;
+  variantName?: string | null;
+  variant_set_id?: string | null;
+  variantSetDbId?: string | null;
+  genotype?: string | null;
+  genotypeValue?: string | null;
+  read_depth?: number | null;
+  phase_set?: string | null;
+}

frontend/src/app/(app)/genotyping/genome-map/api.ts

@@ -0,0 +1,568 @@
+import { DEFAULT_LIST_PAGE_SIZE, DEFAULT_PAGE_QUERY } from "@/constants/api";
+import { createCachedLoader, loadCommonCropNameOptions, type SelectOption as CachedSelectOption } from "@/services/dropdownCache";
+import { getAuthToken } from "@/utils/token";
+import { readAdditionalInfoString } from "./genomeMapUtils";
+import {
+  NONE_SELECT_VALUE,
+  type GenomeMapDetail,
+  type GenomeMapQuery,
+  type GenomeMapRecord,
+  type LinkageGroupQuery,
+  type LinkageGroupRecord,
+  type MarkerPositionQuery,
+  type MarkerPositionRecord,
+  type SelectOption,
+} 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;
+}
+
+type GenomeMapPayload = Partial<Record<
+  | "id"
+  | "map_name"
+  | "map_pui"
+  | "common_crop_name"
+  | "scientific_name"
+  | "type"
+  | "unit"
+  | "comments"
+  | "documentation_url"
+  | "published_date",
+  unknown
+>>;
+
+type LinkageGroupPayload = Partial<Record<
+  "id" | "linkage_group_name" | "max_position",
+  unknown
+>>;
+
+type MarkerPositionPayload = Partial<Record<
+  "id" | "linkage_group_id" | "variant_id" | "position",
+  unknown
+>>;
+
+interface VariantLookup {
+  variantDbId?: string;
+  variantId?: string;
+  id?: string;
+  variantNames?: string[] | null;
+  variantName?: string | null;
+}
+
+const readVariantLabel = (item: VariantLookup) =>
+  item.variantNames?.[0] || item.variantName || item.variantDbId || item.variantId || item.id || "";
+
+const toValidSelectOptions = (options: SelectOption[]) =>
+  options.filter((option) => Boolean(String(option.value ?? "").trim()));
+
+const mapVariantOptions = (rows: VariantLookup[]): SelectOption[] =>
+  toValidSelectOptions(rows.map((item) => {
+    const value = String(item.variantDbId ?? item.variantId ?? item.id ?? "").trim();
+    return { value, label: readVariantLabel(item) || value };
+  }).filter((item) => item.value));
+
+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}`);
+  }
+  if (response.status === 204) {
+    return undefined as T;
+  }
+  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 optionalNumber = (value: unknown) => {
+  if (value === null || value === undefined || value === "") return null;
+  const parsed = Number(value);
+  if (Number.isNaN(parsed)) throw new Error("请输入有效数字");
+  return parsed;
+};
+
+const requiredNumber = (value: unknown, message: string) => {
+  const parsed = optionalNumber(value);
+  if (parsed === null) throw new Error(message);
+  return parsed;
+};
+
+const mapGenomeMap = (item: GenomeMapRecord): GenomeMapRecord => ({
+  ...item,
+  id: item.mapDbId || item.id,
+  map_name: item.map_name ?? item.mapName ?? null,
+  map_pui: item.map_pui ?? item.mapPUI ?? null,
+  common_crop_name: item.common_crop_name ?? item.commonCropName ?? null,
+  scientific_name: item.scientific_name ?? item.scientificName ?? null,
+  documentation_url: item.documentation_url ?? item.documentationURL ?? null,
+  published_date: item.published_date ?? (item.publishedDate ? String(item.publishedDate).slice(0, 10) : null),
+  linkage_group_count: item.linkage_group_count ?? item.linkageGroupCount ?? null,
+  marker_count: item.marker_count ?? item.markerCount ?? null,
+});
+
+const mapLinkageGroup = (item: Record<string, unknown>): LinkageGroupRecord => {
+  const id = (
+    readAdditionalInfoString(item, "linkageGroupDbId")
+    || String(item.linkageGroupDbId ?? item.id ?? "")
+  ).trim();
+  const mapDbId = readAdditionalInfoString(item, "mapDbId") || String(item.mapDbId ?? item.map_db_id ?? "").trim();
+  return {
+    ...item,
+    id,
+    linkage_group_db_id: id,
+    linkage_group_name: String(item.linkageGroupName ?? item.linkage_group_name ?? ""),
+    max_position: (item.maxPosition ?? item.max_position) as number | null,
+    marker_count: (item.markerCount ?? item.marker_count) as number | null,
+    map_db_id: mapDbId || undefined,
+  };
+};
+
+const mapMarkerPosition = (item: Record<string, unknown>): MarkerPositionRecord => {
+  const id = readAdditionalInfoString(item, "markerPositionDbId")
+    || String(item.markerPositionDbId ?? item.id ?? "");
+  return {
+    ...item,
+    id,
+    marker_position_db_id: id,
+    linkage_group_db_id: readAdditionalInfoString(item, "linkageGroupDbId") ?? undefined,
+    linkage_group_name: String(item.linkageGroupName ?? item.linkage_group_name ?? ""),
+    variant_db_id: String(item.variantDbId ?? item.variant_db_id ?? ""),
+    variant_name: String(item.variantName ?? item.variant_name ?? ""),
+    position: (item.position ?? null) as number | null,
+    map_db_id: String(item.mapDbId ?? item.map_db_id ?? ""),
+    map_name: String(item.mapName ?? item.map_name ?? ""),
+  };
+};
+
+const genomeMapBody = (payload: GenomeMapPayload) => ({
+  mapDbId: optionalText(payload.id),
+  mapName: requiredText(payload.map_name, "图谱名称不能为空"),
+  commonCropName: optionalText(payload.common_crop_name),
+  scientificName: optionalText(payload.scientific_name),
+  type: optionalText(payload.type),
+  unit: optionalText(payload.unit),
+  comments: optionalText(payload.comments),
+  documentationURL: optionalText(payload.documentation_url),
+  publishedDate: optionalText(payload.published_date),
+});
+
+const linkageGroupBody = (payload: LinkageGroupPayload) => ({
+  linkageGroupName: requiredText(payload.linkage_group_name, "连锁群名称不能为空"),
+  maxPosition: optionalNumber(payload.max_position),
+});
+
+const markerPositionBody = (payload: MarkerPositionPayload) => ({
+  markerPositionDbId: optionalText(payload.id),
+  linkageGroupDbId: requiredText(payload.linkage_group_id, "请选择连锁群"),
+  variantDbId: requiredText(payload.variant_id, "请选择 Variant"),
+  position: requiredNumber(payload.position, "位置不能为空"),
+});
+
+export const normalizeGenomeMapFormData = (row: GenomeMapRecord) => ({
+  id: row.id,
+  map_name: row.map_name || "",
+  map_pui: row.map_pui || "",
+  common_crop_name: row.common_crop_name && row.common_crop_name !== NONE_SELECT_VALUE
+    ? row.common_crop_name
+    : NONE_SELECT_VALUE,
+  scientific_name: row.scientific_name || "",
+  type: row.type || "",
+  unit: row.unit || "",
+  comments: row.comments || "",
+  documentation_url: row.documentation_url || "",
+  published_date: row.published_date || "",
+});
+
+export const normalizeLinkageGroupFormData = (row: LinkageGroupRecord, includeMap = false) => ({
+  id: row.id,
+  linkage_group_name: row.linkage_group_name || "",
+  max_position: row.max_position ?? "",
+  ...(includeMap ? {
+    map_db_id: row.map_db_id && row.map_db_id !== NONE_SELECT_VALUE
+      ? row.map_db_id
+      : NONE_SELECT_VALUE,
+  } : {}),
+});
+
+export const normalizeMarkerPositionFormData = (row: MarkerPositionRecord) => ({
+  id: row.id,
+  linkage_group_id: row.linkage_group_db_id && row.linkage_group_db_id !== NONE_SELECT_VALUE
+    ? row.linkage_group_db_id
+    : NONE_SELECT_VALUE,
+  variant_id: row.variant_db_id && row.variant_db_id !== NONE_SELECT_VALUE
+    ? row.variant_db_id
+    : NONE_SELECT_VALUE,
+  position: row.position ?? "",
+});
+
+const mapListLoader = createCachedLoader(async () => {
+  const response = await request<BrapiListResponse<GenomeMapRecord>>(`/brapi/v2/maps?${DEFAULT_PAGE_QUERY}`);
+  return response.result.data.map(mapGenomeMap);
+});
+
+const allLinkageGroupsLoader = createCachedLoader(async () => {
+  const maps = await mapListLoader.load();
+  if (maps.length === 0) return [];
+  const batches = await Promise.all(
+    maps.map(async (map) => {
+      try {
+        const rows = await fetchLinkageGroupRows(map.id);
+        return rows
+          .filter((row) => row.id)
+          .map((row) => ({
+            ...row,
+            map_db_id: row.map_db_id || map.id,
+            map_name: map.map_name || map.id,
+          }));
+      } catch {
+        return [];
+      }
+    }),
+  );
+  return batches.flat();
+});
+
+const variantListLoader = createCachedLoader(async () => {
+  const response = await request<BrapiListResponse<VariantLookup>>(
+    `/brapi/v2/variants?pageToken=0&pageSize=${DEFAULT_LIST_PAGE_SIZE}`,
+  );
+  return mapVariantOptions(response.result?.data ?? []);
+});
+
+export function invalidateGenomeMapPageCache() {
+  mapListLoader.invalidate();
+  allLinkageGroupsLoader.invalidate();
+  variantListLoader.invalidate();
+}
+
+const filterLinkageGroupRows = (rows: LinkageGroupRecord[], query?: LinkageGroupQuery) => {
+  const nameFilter = String(query?.linkage_group_name ?? "").trim().toLowerCase();
+  const mapFilter = optionalText(query?.map_db_id);
+  return rows.filter((row) => {
+    if (nameFilter && !String(row.linkage_group_name ?? "").toLowerCase().includes(nameFilter)) return false;
+    if (mapFilter && row.map_db_id !== mapFilter) return false;
+    return true;
+  });
+};
+
+export async function loadLinkageGroupPageData(params: {
+  query?: LinkageGroupQuery;
+  force?: boolean;
+} = {}) {
+  const [maps, linkageGroups] = await Promise.all([
+    mapListLoader.load(params.force),
+    allLinkageGroupsLoader.load(params.force),
+  ]);
+  const mapOptions: SelectOption[] = maps.map((map) => ({
+    value: map.id,
+    label: map.map_name || map.id,
+  }));
+  return {
+    options: { maps: mapOptions },
+    rows: filterLinkageGroupRows(linkageGroups, params.query),
+  };
+}
+
+const filterMapRows = (rows: GenomeMapRecord[], query?: GenomeMapQuery) => {
+  const nameFilter = String(query?.map_name ?? "").trim().toLowerCase();
+  const cropFilter = optionalText(query?.common_crop_name);
+  const typeFilter = optionalText(query?.type);
+  return rows.filter((row) => {
+    if (nameFilter && !String(row.map_name ?? "").toLowerCase().includes(nameFilter)) return false;
+    if (cropFilter && row.common_crop_name !== cropFilter) return false;
+    if (typeFilter && row.type !== typeFilter) return false;
+    return true;
+  });
+};
+
+export async function loadGenomeMapPageData(params: {
+  query?: GenomeMapQuery;
+  force?: boolean;
+} = {}) {
+  const [maps, cropOptions] = await Promise.all([
+    mapListLoader.load(params.force),
+    loadCommonCropNameOptions(params.force),
+  ]);
+  const cropSelectOptions: SelectOption[] = cropOptions.map((item: CachedSelectOption) => ({
+    value: item.value,
+    label: item.label,
+  }));
+  return {
+    options: { crops: cropSelectOptions },
+    rows: filterMapRows(maps, params.query),
+  };
+}
+
+export async function fetchGenomeMapDetail(mapDbId: string): Promise<GenomeMapDetail> {
+  const [mapResponse, linkageResponse, markerResponse] = await Promise.all([
+    request<BrapiSingleResponse<GenomeMapRecord>>(`/brapi/v2/maps/${encodeURIComponent(mapDbId)}`),
+    request<BrapiListResponse<Record<string, unknown>>>(
+      `/brapi/v2/maps/${encodeURIComponent(mapDbId)}/linkagegroups?${DEFAULT_PAGE_QUERY}`,
+    ),
+    request<BrapiListResponse<Record<string, unknown>>>(
+      `/brapi/v2/markerpositions?mapDbId=${encodeURIComponent(mapDbId)}&${DEFAULT_PAGE_QUERY}`,
+    ),
+  ]);
+  const map = mapGenomeMap(mapResponse.result);
+  return {
+    ...map,
+    linkageGroups: linkageResponse.result.data.map(mapLinkageGroup),
+    markerPositions: markerResponse.result.data.map(mapMarkerPosition),
+  };
+}
+
+export async function fetchLinkageGroupRows(mapDbId: string): Promise<LinkageGroupRecord[]> {
+  const response = await request<BrapiListResponse<Record<string, unknown>>>(
+    `/brapi/v2/maps/${encodeURIComponent(mapDbId)}/linkagegroups?${DEFAULT_PAGE_QUERY}`,
+  );
+  return response.result.data.map(mapLinkageGroup);
+}
+
+const buildMarkerPositionQueryString = (query?: MarkerPositionQuery) => {
+  const params = new URLSearchParams(DEFAULT_PAGE_QUERY);
+  const mapDbId = optionalText(query?.map_db_id);
+  const linkageGroupName = optionalText(query?.linkage_group_name);
+  const variantDbId = optionalText(query?.variant_db_id);
+  if (mapDbId) params.set("mapDbId", mapDbId);
+  if (linkageGroupName) params.set("linkageGroupName", linkageGroupName);
+  if (variantDbId) params.set("variantDbId", variantDbId);
+  return params.toString();
+};
+
+const filterMarkerPositionRows = (
+  rows: MarkerPositionRecord[],
+  query?: MarkerPositionQuery,
+  linkageGroupDbId?: string,
+) => {
+  const linkageGroupFilter = optionalText(linkageGroupDbId);
+  return rows.filter((row) => {
+    if (linkageGroupFilter && row.linkage_group_db_id !== linkageGroupFilter) return false;
+    return true;
+  });
+};
+
+export async function fetchMarkerPositionRowsByQuery(
+  query?: MarkerPositionQuery,
+  linkageGroupDbId?: string,
+): Promise<MarkerPositionRecord[]> {
+  const response = await request<BrapiListResponse<Record<string, unknown>>>(
+    `/brapi/v2/markerpositions?${buildMarkerPositionQueryString(query)}`,
+  );
+  return filterMarkerPositionRows(
+    response.result.data.map(mapMarkerPosition),
+    query,
+    linkageGroupDbId,
+  );
+}
+
+export async function loadMarkerPositionFilterOptions(params: {
+  mapDbId?: string;
+} = {}) {
+  const maps = await mapListLoader.load();
+  const mapOptions: SelectOption[] = maps.map((map) => ({
+    value: map.id,
+    label: map.map_name || map.id,
+  }));
+  const mapFilter = optionalText(params.mapDbId);
+  let linkageGroupOptions: SelectOption[] = [];
+  if (mapFilter) {
+    const rows = await fetchLinkageGroupRows(mapFilter);
+    linkageGroupOptions = toValidSelectOptions(rows.map((row) => ({
+      value: row.linkage_group_name || row.id,
+      label: row.linkage_group_name || row.id,
+    })));
+  } else {
+    const linkageGroups = await allLinkageGroupsLoader.load();
+    linkageGroupOptions = toValidSelectOptions(linkageGroups.map((row) => ({
+      value: row.linkage_group_name || row.id,
+      label: row.map_name
+        ? `${row.linkage_group_name || row.id} (${row.map_name})`
+        : (row.linkage_group_name || row.id),
+    })));
+  }
+  const variants = await variantListLoader.load();
+  return {
+    maps: mapOptions,
+    linkageGroups: linkageGroupOptions,
+    variants,
+  };
+}
+
+export async function loadMarkerPositionPageData(params: {
+  query?: MarkerPositionQuery;
+} = {}) {
+  const mapDbId = optionalText(params.query?.map_db_id) ?? undefined;
+  const [options, rows] = await Promise.all([
+    loadMarkerPositionFilterOptions({ mapDbId }),
+    fetchMarkerPositionRowsByQuery(params.query),
+  ]);
+  return { options, rows };
+}
+
+export async function fetchLinkageGroupDetail(
+  mapDbId: string,
+  linkageGroupDbId: string,
+): Promise<LinkageGroupRecord | null> {
+  const rows = await fetchLinkageGroupRows(mapDbId);
+  return rows.find((row) => row.id === linkageGroupDbId) ?? null;
+}
+
+export async function fetchMarkerPositionRows(mapDbId: string): Promise<MarkerPositionRecord[]> {
+  return fetchMarkerPositionRowsByQuery({ map_db_id: mapDbId });
+}
+
+export async function fetchMarkerPositionsByVariantId(variantDbId: string): Promise<MarkerPositionRecord[]> {
+  return fetchMarkerPositionRowsByQuery({ variant_db_id: variantDbId });
+}
+
+export async function fetchVariantOptions(force = false): Promise<SelectOption[]> {
+  return variantListLoader.load(force);
+}
+
+export async function fetchAllLinkageGroupFormOptions(): Promise<SelectOption[]> {
+  const linkageGroups = await allLinkageGroupsLoader.load();
+  return toValidSelectOptions(linkageGroups.map((row) => ({
+    value: row.id,
+    label: row.map_name
+      ? `${row.linkage_group_name || row.id} (${row.map_name})`
+      : (row.linkage_group_name || row.id),
+  })));
+}
+
+export async function fetchLinkageGroupOptions(mapDbId: string): Promise<SelectOption[]> {
+  const rows = await fetchLinkageGroupRows(mapDbId);
+  return toValidSelectOptions(rows.map((row) => ({
+    value: row.id,
+    label: row.linkage_group_name || row.id,
+  })));
+}
+
+export async function createGenomeMapRow(payload: GenomeMapPayload) {
+  invalidateGenomeMapPageCache();
+  const response = await request<BrapiListResponse<GenomeMapRecord>>("/brapi/v2/maps", {
+    method: "POST",
+    body: JSON.stringify(genomeMapBody(payload)),
+  });
+  return mapGenomeMap(response.result.data[0]);
+}
+
+export async function updateGenomeMapRow(id: string, payload: GenomeMapPayload) {
+  invalidateGenomeMapPageCache();
+  const response = await request<BrapiSingleResponse<GenomeMapRecord>>(
+    `/brapi/v2/maps/${encodeURIComponent(id)}`,
+    { method: "PUT", body: JSON.stringify(genomeMapBody(payload)) },
+  );
+  return mapGenomeMap(response.result);
+}
+
+export async function deleteGenomeMapRow(id: string) {
+  invalidateGenomeMapPageCache();
+  await request(`/brapi/v2/maps/${encodeURIComponent(id)}`, { method: "DELETE" });
+}
+
+export async function createLinkageGroupRow(mapDbId: string, payload: LinkageGroupPayload) {
+  invalidateGenomeMapPageCache();
+  const response = await request<BrapiListResponse<Record<string, unknown>>>(
+    `/brapi/v2/maps/${encodeURIComponent(mapDbId)}/linkagegroups`,
+    { method: "POST", body: JSON.stringify(linkageGroupBody(payload)) },
+  );
+  return mapLinkageGroup(response.result.data[0]);
+}
+
+export async function createLinkageGroupRowFromPayload(payload: LinkageGroupPayload & { map_db_id?: unknown }) {
+  const mapDbId = requiredText(payload.map_db_id, "请选择所属图谱");
+  return createLinkageGroupRow(mapDbId, payload);
+}
+
+export async function updateLinkageGroupRow(
+  mapDbId: string,
+  linkageGroupDbId: string,
+  payload: LinkageGroupPayload,
+) {
+  invalidateGenomeMapPageCache();
+  const response = await request<BrapiListResponse<Record<string, unknown>>>(
+    `/brapi/v2/maps/${encodeURIComponent(mapDbId)}/linkagegroups/${encodeURIComponent(linkageGroupDbId)}`,
+    { method: "PUT", body: JSON.stringify(linkageGroupBody(payload)) },
+  );
+  return mapLinkageGroup(response.result.data[0]);
+}
+
+export async function deleteLinkageGroupRow(mapDbId: string, linkageGroupDbId: string) {
+  invalidateGenomeMapPageCache();
+  await request(
+    `/brapi/v2/maps/${encodeURIComponent(mapDbId)}/linkagegroups/${encodeURIComponent(linkageGroupDbId)}`,
+    { method: "DELETE" },
+  );
+}
+
+export async function createMarkerPositionRow(payload: MarkerPositionPayload) {
+  invalidateGenomeMapPageCache();
+  const response = await request<BrapiListResponse<Record<string, unknown>>>("/brapi/v2/markerpositions", {
+    method: "POST",
+    body: JSON.stringify(markerPositionBody(payload)),
+  });
+  return mapMarkerPosition(response.result.data[0]);
+}
+
+export async function updateMarkerPositionRow(id: string, payload: MarkerPositionPayload) {
+  invalidateGenomeMapPageCache();
+  const response = await request<BrapiListResponse<Record<string, unknown>>>(
+    `/brapi/v2/markerpositions/${encodeURIComponent(id)}`,
+    { method: "PUT", body: JSON.stringify(markerPositionBody(payload)) },
+  );
+  return mapMarkerPosition(response.result.data[0]);
+}
+
+export async function deleteMarkerPositionRow(id: string) {
+  invalidateGenomeMapPageCache();
+  await request(`/brapi/v2/markerpositions/${encodeURIComponent(id)}`, { method: "DELETE" });
+}

frontend/src/app/(app)/genotyping/genome-map/components/GenomeMapTab.tsx

@@ -0,0 +1,196 @@
+"use client";
+
+import Link from "next/link";
+import { useCallback, useMemo, useState } from "react";
+import { Map, 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 {
+  createGenomeMapRow,
+  deleteGenomeMapRow,
+  loadGenomeMapPageData,
+  normalizeGenomeMapFormData,
+  updateGenomeMapRow,
+} from "../api";
+import { NONE_SELECT_VALUE, type GenomeMapQuery, type SelectOption } from "../types";
+
+const mapTypeOptions: SelectOption[] = [
+  { value: "physical", label: "physical（物理图）" },
+  { value: "genomic", label: "genomic（基因组图）" },
+];
+
+const emptyQuery = (): GenomeMapQuery => ({
+  map_name: "",
+  common_crop_name: NONE_SELECT_VALUE,
+  type: NONE_SELECT_VALUE,
+});
+
+const optionOrNone = (label: string, options: SelectOption[]) => [
+  { value: NONE_SELECT_VALUE, label },
+  ...options,
+];
+
+export function GenomeMapTab() {
+  const [cropOptions, setCropOptions] = useState<SelectOption[]>([]);
+  const [draftQuery, setDraftQuery] = useState<GenomeMapQuery>(emptyQuery);
+  const [appliedQuery, setAppliedQuery] = useState<GenomeMapQuery>(emptyQuery);
+
+  const loadRows = useCallback(async () => {
+    const { options, rows } = await loadGenomeMapPageData({ query: appliedQuery });
+    setCropOptions(options.crops);
+    return rows as unknown as Record<string, unknown>[];
+  }, [appliedQuery]);
+
+  const fields = useMemo<BrapiFormField[]>(() => [
+    { key: "id", label: "Map ID", type: "text", placeholder: "留空则系统自动生成" },
+    { key: "map_name", label: "图谱名称", type: "text", required: true, placeholder: "如 Maize IBM2" },
+    {
+      key: "map_pui",
+      label: "Map PUI",
+      type: "text",
+      readOnly: true,
+      placeholder: "保存后由系统自动生成",
+    },
+    {
+      key: "common_crop_name",
+      label: "作物",
+      type: "select",
+      options: optionOrNone("不关联作物", cropOptions),
+    },
+    { key: "scientific_name", label: "学名", type: "text", placeholder: "Zea mays" },
+    {
+      key: "type",
+      label: "图谱类型",
+      type: "select",
+      options: optionOrNone("不指定", mapTypeOptions),
+    },
+    { key: "unit", label: "单位", type: "text", placeholder: "如 cM" },
+    { key: "published_date", label: "发表日期", type: "date" },
+    { key: "documentation_url", label: "文档 URL", type: "text", placeholder: "https://..." },
+    { key: "comments", label: "备注", type: "textarea", colSpan: 2 },
+  ], [cropOptions]);
+
+  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">图谱名称</Label>
+          <Input
+            value={draftQuery.map_name ?? ""}
+            onChange={(event) => setDraftQuery((current) => ({ ...current, map_name: event.target.value }))}
+            placeholder="mapName 模糊匹配"
+          />
+        </div>
+        <div className="space-y-1.5">
+          <Label className="text-xs text-slate-500">作物</Label>
+          <Select
+            value={draftQuery.common_crop_name ?? NONE_SELECT_VALUE}
+            onValueChange={(value) => setDraftQuery((current) => ({ ...current, common_crop_name: value }))}
+          >
+            <SelectTrigger><SelectValue placeholder="全部" /></SelectTrigger>
+            <SelectContent>
+              <SelectItem value={NONE_SELECT_VALUE}>全部</SelectItem>
+              {cropOptions.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">类型</Label>
+          <Select
+            value={draftQuery.type ?? NONE_SELECT_VALUE}
+            onValueChange={(value) => setDraftQuery((current) => ({ ...current, type: value }))}
+          >
+            <SelectTrigger><SelectValue placeholder="全部" /></SelectTrigger>
+            <SelectContent>
+              <SelectItem value={NONE_SELECT_VALUE}>全部</SelectItem>
+              {mapTypeOptions.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, cropOptions]);
+
+  return (
+    <BrapiEntityPage
+      useEnhancedDialog
+      icon={Map}
+      iconBg="bg-gradient-to-br from-teal-500 to-cyan-600"
+      title="GenomeMap 遗传图谱"
+      description="维护遗传图谱主数据；可切换 Linkage Group Tab 跨图谱维护，或进入详情维护 Marker Position。"
+      addLabel="新增图谱"
+      columns={[
+        {
+          key: "map_name",
+          label: "名称",
+          render: (value, row) => {
+            const id = String(row.id ?? row.mapDbId ?? "");
+            const name = String(value ?? "—");
+            if (!id) return name;
+            return (
+              <Link
+                href={`/genotyping/genome-map/maps/${encodeURIComponent(id)}`}
+                className="font-medium text-teal-600 hover:underline dark:text-teal-400"
+              >
+                {name}
+              </Link>
+            );
+          },
+        },
+        { key: "common_crop_name", label: "作物" },
+        { key: "type", label: "类型" },
+        { key: "unit", label: "单位" },
+        {
+          key: "linkage_group_count",
+          label: "连锁群",
+          render: (value) => <Badge variant="outline">{Number(value ?? 0)}</Badge>,
+        },
+        {
+          key: "marker_count",
+          label: "Marker 数",
+          render: (value) => <Badge variant="outline">{Number(value ?? 0)}</Badge>,
+        },
+      ]}
+      fields={fields}
+      data={[]}
+      stats={[{
+        label: "/brapi/v2/maps",
+        value: "BrAPI",
+        className: "bg-teal-50 text-teal-700 dark:bg-teal-400/10 dark:text-teal-200",
+      }]}
+      loadData={loadRows}
+      fetchRecord={async (id) => {
+        const { rows } = await loadGenomeMapPageData({ force: true });
+        const row = rows.find((item) => item.id === id);
+        if (!row) throw new Error("图谱不存在");
+        return normalizeGenomeMapFormData(row);
+      }}
+      createRecord={(payload) => createGenomeMapRow(payload) as unknown as Promise<Record<string, unknown>>}
+      updateRecord={(id, payload) => updateGenomeMapRow(id, payload) as unknown as Promise<Record<string, unknown>>}
+      deleteRecord={deleteGenomeMapRow}
+      renderQueryForm={renderQueryForm}
+    />
+  );
+}

frontend/src/app/(app)/genotyping/genome-map/components/LinkageGroupEntityPage.tsx

@@ -0,0 +1,221 @@
+"use client";
+
+import Link from "next/link";
+import { useCallback, useMemo, type ReactNode } from "react";
+import { GitBranch } from "lucide-react";
+import { BrapiEntityPage, type BrapiFormField } from "@/components/brapi/BrapiEntityPage";
+import { Badge } from "@/components/ui/badge";
+import { Input } from "@/components/ui/input";
+import { Label } from "@/components/ui/label";
+import {
+  createLinkageGroupRow,
+  createLinkageGroupRowFromPayload,
+  deleteLinkageGroupRow,
+  fetchLinkageGroupRows,
+  loadLinkageGroupPageData,
+  normalizeLinkageGroupFormData,
+  updateLinkageGroupRow,
+} from "../api";
+import { NONE_SELECT_VALUE, type LinkageGroupQuery, type SelectOption } from "../types";
+
+const optionOrNone = (label: string, options: SelectOption[]) => [
+  { value: NONE_SELECT_VALUE, label },
+  ...options,
+];
+
+interface LinkageGroupEntityPageProps {
+  /** 详情页固定所属图谱；入口 Tab 不传则跨图谱列表维护 */
+  mapDbId?: string;
+  mapOptions?: SelectOption[];
+  linkageGroupQuery?: LinkageGroupQuery;
+  onChanged?: () => void;
+  defaultFormValues?: Record<string, unknown>;
+  renderQueryForm?: () => ReactNode;
+}
+
+export function LinkageGroupEntityPage({
+  mapDbId,
+  mapOptions = [],
+  linkageGroupQuery,
+  onChanged,
+  defaultFormValues,
+  renderQueryForm,
+}: LinkageGroupEntityPageProps) {
+  const scopedToMap = Boolean(mapDbId);
+  const includeMapInForm = !scopedToMap;
+
+  const loadRows = useCallback(async () => {
+    if (scopedToMap && mapDbId) {
+      const rows = await fetchLinkageGroupRows(mapDbId);
+      return rows as unknown as Record<string, unknown>[];
+    }
+    const { rows } = await loadLinkageGroupPageData({ query: linkageGroupQuery });
+    return rows as unknown as Record<string, unknown>[];
+  }, [scopedToMap, mapDbId, linkageGroupQuery]);
+
+  const resolveMapDbId = useCallback((payload: Record<string, unknown>, row?: Record<string, unknown>) => {
+    if (mapDbId) return mapDbId;
+    const fromPayload = String(payload.map_db_id ?? "").trim();
+    if (fromPayload && fromPayload !== NONE_SELECT_VALUE) return fromPayload;
+    return String(row?.map_db_id ?? row?.mapDbId ?? "").trim();
+  }, [mapDbId]);
+
+  const fields = useMemo<BrapiFormField[]>(() => {
+    const base: BrapiFormField[] = [];
+    if (includeMapInForm) {
+      base.push({
+        key: "map_db_id",
+        label: "所属图谱",
+        type: "select",
+        required: true,
+        options: optionOrNone("请选择图谱", mapOptions),
+      });
+    }
+    base.push(
+      { key: "linkage_group_name", label: "连锁群名称", type: "text", required: true, placeholder: "如 Chr01" },
+      { key: "max_position", label: "最大位置", type: "number", placeholder: "可选，非负整数" },
+    );
+    return base;
+  }, [includeMapInForm, mapOptions]);
+
+  const columns = useMemo(() => {
+    const cols = [
+      {
+        key: "linkage_group_name",
+        label: "名称",
+        render: (value: unknown, row: Record<string, unknown>) => {
+          const name = String(value ?? "—");
+          const targetMapId = resolveMapDbId({}, row);
+          if (!targetMapId) return name;
+          return (
+            <Link
+              href={`/genotyping/genome-map/maps/${encodeURIComponent(targetMapId)}/linkage-groups/${encodeURIComponent(String(row.id ?? ""))}`}
+              className="font-medium text-teal-600 hover:underline dark:text-teal-400"
+            >
+              {name}
+            </Link>
+          );
+        },
+      },
+    ];
+    if (!scopedToMap) {
+      cols.push({
+        key: "map_name",
+        label: "所属图谱",
+        render: (value: unknown, row: Record<string, unknown>) => {
+          const targetMapId = resolveMapDbId({}, row);
+          const label = String(value ?? row.map_name ?? "—");
+          if (!targetMapId) return label;
+          return (
+            <Link
+              href={`/genotyping/genome-map/maps/${encodeURIComponent(targetMapId)}`}
+              className="text-teal-600 hover:underline dark:text-teal-400"
+            >
+              {label}
+            </Link>
+          );
+        },
+      });
+    }
+    cols.push(
+      { key: "max_position", label: "最大位置", render: (value: unknown) => String(value ?? "—") },
+      {
+        key: "marker_count",
+        label: "Marker 数",
+        render: (value: unknown) => <Badge variant="outline">{Number(value ?? 0)}</Badge>,
+      },
+    );
+    return cols;
+  }, [scopedToMap, resolveMapDbId]);
+
+  const wrapMutation = useCallback(<T, >(action: () => Promise<T>) => async () => {
+    const result = await action();
+    onChanged?.();
+    return result;
+  }, [onChanged]);
+
+  return (
+    <BrapiEntityPage
+      useEnhancedDialog
+      icon={GitBranch}
+      iconBg="bg-gradient-to-br from-teal-500 to-emerald-600"
+      title={scopedToMap ? "连锁群 Linkage Group" : "Linkage Group 连锁群"}
+      description={
+        scopedToMap
+          ? "该图谱下的连锁群；删除前请确认无 Marker Position 引用。"
+          : "跨图谱维护连锁群；新增时需选择所属 GenomeMap，也可在图谱详情中维护。"
+      }
+      addLabel="新增连锁群"
+      defaultFormValues={defaultFormValues}
+      columns={columns}
+      fields={fields}
+      data={[]}
+      stats={[{
+        label: scopedToMap ? `/maps/${mapDbId}/linkagegroups` : "聚合 /maps/*/linkagegroups",
+        value: "BrAPI",
+        className: "bg-emerald-50 text-emerald-700 dark:bg-emerald-400/10 dark:text-emerald-200",
+      }]}
+      loadData={loadRows}
+      fetchRecord={async (id) => {
+        if (scopedToMap && mapDbId) {
+          const rows = await fetchLinkageGroupRows(mapDbId);
+          const row = rows.find((item) => item.id === id);
+          if (!row) throw new Error("连锁群不存在");
+          return normalizeLinkageGroupFormData(row);
+        }
+        const { rows } = await loadLinkageGroupPageData({ force: true });
+        const row = rows.find((item) => item.id === id);
+        if (!row) throw new Error("连锁群不存在");
+        return normalizeLinkageGroupFormData(row, true);
+      }}
+      createRecord={(payload) => {
+        if (scopedToMap && mapDbId) {
+          return wrapMutation(() => createLinkageGroupRow(mapDbId, payload))() as Promise<Record<string, unknown>>;
+        }
+        return wrapMutation(() => createLinkageGroupRowFromPayload(payload))() as Promise<Record<string, unknown>>;
+      }}
+      updateRecord={async (id, payload) => {
+        const targetMapId = resolveMapDbId(payload);
+        if (!targetMapId) throw new Error("无法确定所属图谱");
+        return wrapMutation(() => updateLinkageGroupRow(targetMapId, id, payload))() as Promise<Record<string, unknown>>;
+      }}
+      deleteRecord={async (id) => {
+        let targetMapId = mapDbId;
+        if (!targetMapId) {
+          const { rows } = await loadLinkageGroupPageData({ force: true });
+          const row = rows.find((item) => item.id === id);
+          targetMapId = row?.map_db_id || undefined;
+        }
+        if (!targetMapId) throw new Error("无法确定所属图谱");
+        await wrapMutation(() => deleteLinkageGroupRow(targetMapId, id))();
+      }}
+      renderQueryForm={renderQueryForm}
+      renderFormExtra={({ editingRow }) => (
+        <>
+          <div className="md:col-span-2 space-y-1.5">
+            <Label className="text-sm text-slate-700 dark:text-slate-200">LinkageGroup ID</Label>
+            {editingRow ? (
+              <Input
+                value={String(editingRow.id ?? "")}
+                readOnly
+                disabled
+                className="bg-slate-50 dark:bg-slate-900"
+              />
+            ) : (
+              <p className="rounded-md border border-dashed border-slate-200 bg-slate-50 px-3 py-2 text-sm text-slate-500 dark:border-slate-700 dark:bg-slate-900 dark:text-slate-400">
+                保存后由系统自动生成
+              </p>
+            )}
+            <p className="text-xs text-slate-500">数据库主键，新增与修改时均不可编辑。</p>
+          </div>
+          <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 className="mt-1 text-emerald-800/80 dark:text-emerald-200/80">
+              同一图谱下连锁群名称不可重复；删除前需无 Marker Position 引用。
+            </p>
+          </div>
+        </>
+      )}
+    />
+  );
+}

frontend/src/app/(app)/genotyping/genome-map/components/LinkageGroupPanel.tsx

@@ -0,0 +1,12 @@
+"use client";
+
+import { LinkageGroupEntityPage } from "./LinkageGroupEntityPage";
+
+interface LinkageGroupPanelProps {
+  mapDbId: string;
+  onChanged?: () => void;
+}
+
+export function LinkageGroupPanel({ mapDbId, onChanged }: LinkageGroupPanelProps) {
+  return <LinkageGroupEntityPage mapDbId={mapDbId} onChanged={onChanged} />;
+}

frontend/src/app/(app)/genotyping/genome-map/components/LinkageGroupTab.tsx

@@ -0,0 +1,104 @@
+"use client";
+
+import { useCallback, useEffect, useMemo, useState } from "react";
+import { useSearchParams } from "next/navigation";
+import { RotateCcw, Search } from "lucide-react";
+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 { loadLinkageGroupPageData } from "../api";
+import { LinkageGroupEntityPage } from "./LinkageGroupEntityPage";
+import { NONE_SELECT_VALUE, type LinkageGroupQuery, type SelectOption } from "../types";
+
+const emptyQuery = (): LinkageGroupQuery => ({
+  linkage_group_name: "",
+  map_db_id: NONE_SELECT_VALUE,
+});
+
+function toSelectValue(value: string | null | undefined) {
+  return value && value !== NONE_SELECT_VALUE ? value : NONE_SELECT_VALUE;
+}
+
+export function LinkageGroupTab() {
+  const searchParams = useSearchParams();
+  const [mapOptions, setMapOptions] = useState<SelectOption[]>([]);
+  const [draftQuery, setDraftQuery] = useState<LinkageGroupQuery>(() => ({
+    ...emptyQuery(),
+    map_db_id: searchParams.get("map_db_id") ?? NONE_SELECT_VALUE,
+  }));
+  const [appliedQuery, setAppliedQuery] = useState<LinkageGroupQuery>(() => ({
+    ...emptyQuery(),
+    map_db_id: searchParams.get("map_db_id") ?? NONE_SELECT_VALUE,
+  }));
+
+  const urlDefaultFormValues = useMemo(() => {
+    const mapDbId = searchParams.get("map_db_id");
+    return mapDbId ? { map_db_id: mapDbId } : undefined;
+  }, [searchParams]);
+
+  useEffect(() => {
+    let mounted = true;
+    loadLinkageGroupPageData().then(({ options }) => {
+      if (!mounted) return;
+      setMapOptions(options.maps);
+    });
+    return () => { mounted = false; };
+  }, []);
+
+  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">连锁群名称</Label>
+          <Input
+            value={draftQuery.linkage_group_name ?? ""}
+            onChange={(event) => setDraftQuery((current) => ({
+              ...current,
+              linkage_group_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">所属图谱</Label>
+          <Select
+            value={toSelectValue(draftQuery.map_db_id)}
+            onValueChange={(value) => setDraftQuery((current) => ({ ...current, map_db_id: value }))}
+          >
+            <SelectTrigger><SelectValue placeholder="全部图谱" /></SelectTrigger>
+            <SelectContent>
+              <SelectItem value={NONE_SELECT_VALUE}>全部图谱</SelectItem>
+              {mapOptions.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, mapOptions]);
+
+  return (
+    <LinkageGroupEntityPage
+      mapOptions={mapOptions}
+      linkageGroupQuery={appliedQuery}
+      defaultFormValues={urlDefaultFormValues}
+      renderQueryForm={renderQueryForm}
+    />
+  );
+}

frontend/src/app/(app)/genotyping/genome-map/components/MarkerPositionEntityPage.tsx

@@ -0,0 +1,222 @@
+"use client";
+
+import Link from "next/link";
+import { useCallback, useEffect, useMemo, useState, type ReactNode } from "react";
+import { MapPin } from "lucide-react";
+import { BrapiEntityPage, type BrapiFormField } from "@/components/brapi/BrapiEntityPage";
+import {
+  createMarkerPositionRow,
+  deleteMarkerPositionRow,
+  fetchAllLinkageGroupFormOptions,
+  fetchLinkageGroupOptions,
+  fetchMarkerPositionRowsByQuery,
+  fetchVariantOptions,
+  normalizeMarkerPositionFormData,
+  updateMarkerPositionRow,
+} from "../api";
+import { NONE_SELECT_VALUE, type MarkerPositionQuery, type SelectOption } from "../types";
+
+interface MarkerPositionEntityPageProps {
+  /** 详情页固定所属图谱 */
+  mapDbId?: string;
+  /** 连锁群详情页固定所属连锁群 */
+  linkageGroupDbId?: string;
+  linkageGroupName?: string | null;
+  markerPositionQuery?: MarkerPositionQuery;
+  onChanged?: () => void;
+  defaultFormValues?: Record<string, unknown>;
+  renderQueryForm?: () => ReactNode;
+}
+
+export function MarkerPositionEntityPage({
+  mapDbId,
+  linkageGroupDbId,
+  linkageGroupName,
+  markerPositionQuery,
+  onChanged,
+  defaultFormValues,
+  renderQueryForm,
+}: MarkerPositionEntityPageProps) {
+  const scopedToMap = Boolean(mapDbId);
+  const scopedToLinkageGroup = Boolean(linkageGroupDbId);
+  const [linkageGroupOptions, setLinkageGroupOptions] = useState<SelectOption[]>([]);
+  const [variantOptions, setVariantOptions] = useState<SelectOption[]>([]);
+
+  useEffect(() => {
+    let mounted = true;
+    const linkagePromise = mapDbId
+      ? fetchLinkageGroupOptions(mapDbId)
+      : fetchAllLinkageGroupFormOptions();
+    Promise.all([linkagePromise, fetchVariantOptions()])
+      .then(([linkageGroups, variants]) => {
+        if (!mounted) return;
+        setLinkageGroupOptions(linkageGroups);
+        setVariantOptions(variants);
+      })
+      .catch(() => {
+        if (!mounted) return;
+        setLinkageGroupOptions([]);
+        setVariantOptions([]);
+      });
+    return () => { mounted = false; };
+  }, [mapDbId]);
+
+  const loadRows = useCallback(async () => {
+    const query = scopedToMap && mapDbId
+      ? { map_db_id: mapDbId }
+      : markerPositionQuery;
+    const rows = await fetchMarkerPositionRowsByQuery(query, linkageGroupDbId);
+    return rows as unknown as Record<string, unknown>[];
+  }, [scopedToMap, mapDbId, linkageGroupDbId, markerPositionQuery]);
+
+  const fields = useMemo<BrapiFormField[]>(() => [
+    { key: "id", label: "MarkerPosition ID", type: "text", placeholder: "留空则系统自动生成" },
+    {
+      key: "linkage_group_id",
+      label: "连锁群",
+      type: "select",
+      required: true,
+      options: [
+        { value: NONE_SELECT_VALUE, label: "请选择连锁群" },
+        ...linkageGroupOptions,
+      ],
+    },
+    {
+      key: "variant_id",
+      label: "Variant",
+      type: "select",
+      required: true,
+      options: [
+        { value: NONE_SELECT_VALUE, label: "请选择 Variant" },
+        ...variantOptions,
+      ],
+    },
+    { key: "position", label: "图谱位置", type: "number", required: true, placeholder: "非负整数" },
+  ], [linkageGroupOptions, variantOptions]);
+
+  const columns = useMemo(() => {
+    const cols = [];
+    if (!scopedToMap) {
+      cols.push({
+        key: "map_name",
+        label: "所属图谱",
+        render: (value: unknown, row: Record<string, unknown>) => {
+          const id = String(row.map_db_id ?? row.mapDbId ?? "");
+          const label = String(value ?? row.map_name ?? "—");
+          if (!id) return label;
+          return (
+            <Link
+              href={`/genotyping/genome-map/maps/${encodeURIComponent(id)}`}
+              className="text-teal-600 hover:underline dark:text-teal-400"
+            >
+              {label}
+            </Link>
+          );
+        },
+      });
+    }
+    cols.push(
+      {
+        key: "linkage_group_name",
+        label: "连锁群",
+        render: (value: unknown, row: Record<string, unknown>) => {
+          const name = String(value ?? "—");
+          const lgId = String(row.linkage_group_db_id ?? row.linkageGroupDbId ?? "");
+          const targetMapId = mapDbId || String(row.map_db_id ?? row.mapDbId ?? "");
+          if (!lgId || !targetMapId) return name;
+          return (
+            <Link
+              href={`/genotyping/genome-map/maps/${encodeURIComponent(targetMapId)}/linkage-groups/${encodeURIComponent(lgId)}`}
+              className="font-medium text-teal-600 hover:underline dark:text-teal-400"
+            >
+              {name}
+            </Link>
+          );
+        },
+      },
+      {
+        key: "variant_name",
+        label: "Variant",
+        render: (value: unknown, row: Record<string, unknown>) => {
+          const id = String(row.variant_db_id ?? row.variantDbId ?? "");
+          const name = String(value ?? "—");
+          if (!id) return name;
+          return (
+            <Link
+              href={`/genotyping/variant/variants/${encodeURIComponent(id)}`}
+              className="font-medium text-rose-600 hover:underline dark:text-rose-400"
+            >
+              {name}
+            </Link>
+          );
+        },
+      },
+      { key: "position", label: "位置" },
+    );
+    return cols;
+  }, [scopedToMap, mapDbId]);
+
+  const resolvedDefaultFormValues = useMemo(() => ({
+    ...defaultFormValues,
+    ...(linkageGroupDbId ? { linkage_group_id: linkageGroupDbId } : {}),
+  }), [defaultFormValues, linkageGroupDbId]);
+
+  const wrapMutation = useCallback(<T, >(action: () => Promise<T>) => async () => {
+    const result = await action();
+    onChanged?.();
+    return result;
+  }, [onChanged]);
+
+  const findRowById = useCallback(async (id: string) => {
+    const query = scopedToMap && mapDbId
+      ? { map_db_id: mapDbId }
+      : markerPositionQuery;
+    const rows = await fetchMarkerPositionRowsByQuery(query, linkageGroupDbId);
+    return rows.find((item) => item.id === id);
+  }, [scopedToMap, mapDbId, linkageGroupDbId, markerPositionQuery]);
+
+  const title = scopedToLinkageGroup && linkageGroupName
+    ? `Marker Position · ${linkageGroupName}`
+    : scopedToMap
+      ? "Marker Position"
+      : "Marker Position 列表";
+
+  const description = scopedToLinkageGroup
+    ? "在该连锁群下维护 Variant 图谱位置；同一 Variant 不可重复。"
+    : scopedToMap
+      ? "将 Variant 定位到连锁群坐标；同一连锁群下同一 Variant 不可重复。"
+      : "按图谱、连锁群、Variant 查询并维护 marker_position。";
+
+  return (
+    <BrapiEntityPage
+      useEnhancedDialog
+      icon={MapPin}
+      iconBg="bg-gradient-to-br from-cyan-500 to-blue-600"
+      title={title}
+      description={description}
+      addLabel="新增 Marker Position"
+      defaultFormValues={resolvedDefaultFormValues}
+      columns={columns}
+      fields={fields}
+      data={[]}
+      loadData={loadRows}
+      fetchRecord={async (id) => {
+        const row = await findRowById(id);
+        if (!row) throw new Error("Marker Position 不存在");
+        return normalizeMarkerPositionFormData(row);
+      }}
+      createRecord={(payload) => wrapMutation(() => createMarkerPositionRow(payload))() as Promise<Record<string, unknown>>}
+      updateRecord={(id, payload) => wrapMutation(() => updateMarkerPositionRow(id, payload))() as Promise<Record<string, unknown>>}
+      deleteRecord={(id) => wrapMutation(() => deleteMarkerPositionRow(id))().then(() => undefined)}
+      renderQueryForm={renderQueryForm}
+      renderFormExtra={() => (
+        <div className="col-span-2 rounded-lg border border-cyan-100 bg-cyan-50/60 p-3 text-xs text-cyan-900 dark:border-cyan-900/40 dark:bg-cyan-950/30 dark:text-cyan-100">
+          <p className="font-medium">校验说明</p>
+          <p className="mt-1 text-cyan-800/80 dark:text-cyan-200/80">
+            position 不应超过所属连锁群的 max_position（若已设置）；单位应与图谱 unit 一致。
+          </p>
+        </div>
+      )}
+    />
+  );
+}

frontend/src/app/(app)/genotyping/genome-map/components/MarkerPositionPanel.tsx

@@ -0,0 +1,12 @@
+"use client";
+
+import { MarkerPositionEntityPage } from "./MarkerPositionEntityPage";
+
+interface MarkerPositionPanelProps {
+  mapDbId: string;
+  onChanged?: () => void;
+}
+
+export function MarkerPositionPanel({ mapDbId, onChanged }: MarkerPositionPanelProps) {
+  return <MarkerPositionEntityPage mapDbId={mapDbId} onChanged={onChanged} />;
+}

frontend/src/app/(app)/genotyping/genome-map/components/MarkerPositionTab.tsx

@@ -0,0 +1,153 @@
+"use client";
+
+import { useCallback, useEffect, useMemo, useState } from "react";
+import { useSearchParams } from "next/navigation";
+import { RotateCcw, Search } from "lucide-react";
+import { Button } from "@/components/ui/button";
+import { Label } from "@/components/ui/label";
+import { Select, SelectContent, SelectItem, SelectTrigger, SelectValue } from "@/components/ui/select";
+import { loadMarkerPositionFilterOptions } from "../api";
+import { MarkerPositionEntityPage } from "./MarkerPositionEntityPage";
+import { NONE_SELECT_VALUE, type MarkerPositionQuery, type SelectOption } from "../types";
+
+const emptyQuery = (): MarkerPositionQuery => ({
+  map_db_id: NONE_SELECT_VALUE,
+  linkage_group_name: NONE_SELECT_VALUE,
+  variant_db_id: NONE_SELECT_VALUE,
+});
+
+function toSelectValue(value: string | null | undefined) {
+  return value && value !== NONE_SELECT_VALUE ? value : NONE_SELECT_VALUE;
+}
+
+export function MarkerPositionTab() {
+  const searchParams = useSearchParams();
+  const [mapOptions, setMapOptions] = useState<SelectOption[]>([]);
+  const [linkageGroupOptions, setLinkageGroupOptions] = useState<SelectOption[]>([]);
+  const [variantOptions, setVariantOptions] = useState<SelectOption[]>([]);
+  const [draftQuery, setDraftQuery] = useState<MarkerPositionQuery>(() => ({
+    ...emptyQuery(),
+    map_db_id: searchParams.get("map_db_id") ?? NONE_SELECT_VALUE,
+    linkage_group_name: searchParams.get("linkage_group_name") ?? NONE_SELECT_VALUE,
+    variant_db_id: searchParams.get("variant_db_id") ?? NONE_SELECT_VALUE,
+  }));
+  const [appliedQuery, setAppliedQuery] = useState<MarkerPositionQuery>(() => ({
+    ...emptyQuery(),
+    map_db_id: searchParams.get("map_db_id") ?? NONE_SELECT_VALUE,
+    linkage_group_name: searchParams.get("linkage_group_name") ?? NONE_SELECT_VALUE,
+    variant_db_id: searchParams.get("variant_db_id") ?? NONE_SELECT_VALUE,
+  }));
+
+  useEffect(() => {
+    let mounted = true;
+    loadMarkerPositionFilterOptions()
+      .then((options) => {
+        if (!mounted) return;
+        setMapOptions(options.maps);
+        setLinkageGroupOptions(options.linkageGroups);
+        setVariantOptions(options.variants);
+      })
+      .catch(() => {
+        if (!mounted) return;
+        setMapOptions([]);
+        setLinkageGroupOptions([]);
+        setVariantOptions([]);
+      });
+    return () => { mounted = false; };
+  }, []);
+
+  useEffect(() => {
+    let mounted = true;
+    const mapDbId = toSelectValue(draftQuery.map_db_id);
+    loadMarkerPositionFilterOptions({
+      mapDbId: mapDbId !== NONE_SELECT_VALUE ? mapDbId : undefined,
+    }).then((options) => {
+      if (!mounted) return;
+      setLinkageGroupOptions(options.linkageGroups);
+    });
+    return () => { mounted = false; };
+  }, [draftQuery.map_db_id]);
+
+  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-3">
+        <div className="space-y-1.5">
+          <Label className="text-xs text-slate-500">所属图谱</Label>
+          <Select
+            value={toSelectValue(draftQuery.map_db_id)}
+            onValueChange={(value) => setDraftQuery((current) => ({
+              ...current,
+              map_db_id: value,
+              linkage_group_name: NONE_SELECT_VALUE,
+            }))}
+          >
+            <SelectTrigger><SelectValue placeholder="全部图谱" /></SelectTrigger>
+            <SelectContent>
+              <SelectItem value={NONE_SELECT_VALUE}>全部图谱</SelectItem>
+              {mapOptions.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">连锁群</Label>
+          <Select
+            value={toSelectValue(draftQuery.linkage_group_name)}
+            onValueChange={(value) => setDraftQuery((current) => ({ ...current, linkage_group_name: value }))}
+          >
+            <SelectTrigger><SelectValue placeholder="全部连锁群" /></SelectTrigger>
+            <SelectContent>
+              <SelectItem value={NONE_SELECT_VALUE}>全部连锁群</SelectItem>
+              {linkageGroupOptions.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">Variant</Label>
+          <Select
+            value={toSelectValue(draftQuery.variant_db_id)}
+            onValueChange={(value) => setDraftQuery((current) => ({ ...current, variant_db_id: value }))}
+          >
+            <SelectTrigger><SelectValue placeholder="全部 Variant" /></SelectTrigger>
+            <SelectContent>
+              <SelectItem value={NONE_SELECT_VALUE}>全部 Variant</SelectItem>
+              {variantOptions.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, mapOptions, linkageGroupOptions, variantOptions]);
+
+  const urlDefaultFormValues = useMemo(() => {
+    const variantId = searchParams.get("variant_db_id");
+    return variantId ? { variant_id: variantId } : undefined;
+  }, [searchParams]);
+
+  return (
+    <MarkerPositionEntityPage
+      markerPositionQuery={appliedQuery}
+      defaultFormValues={urlDefaultFormValues}
+      renderQueryForm={renderQueryForm}
+    />
+  );
+}

frontend/src/app/(app)/genotyping/genome-map/genomeMapUtils.ts

@@ -0,0 +1,15 @@
+export function readAdditionalInfoString(
+  item: Record<string, unknown>,
+  key: string,
+): string | null {
+  const info = item.additionalInfo;
+  if (!info || typeof info !== "object") return null;
+  const value = (info as Record<string, unknown>)[key];
+  return typeof value === "string" && value.trim() ? value.trim() : null;
+}
+
+export function formatPublishedDate(value: unknown): string {
+  if (!value) return "—";
+  const text = String(value);
+  return text.length >= 10 ? text.slice(0, 10) : text;
+}

frontend/src/app/(app)/genotyping/genome-map/maps/[mapDbId]/linkage-groups/[linkageGroupDbId]/page.tsx

@@ -0,0 +1,129 @@
+"use client";
+
+import Link from "next/link";
+import { useCallback, useEffect, useState } from "react";
+import { useParams } from "next/navigation";
+import { ArrowLeft, GitBranch, Map } 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 { MarkerPositionEntityPage } from "../../../../components/MarkerPositionEntityPage";
+import { fetchGenomeMapDetail, fetchLinkageGroupDetail } from "../../../../api";
+import type { GenomeMapRecord, LinkageGroupRecord } from "../../../../types";
+
+export default function LinkageGroupDetailPage() {
+  const params = useParams<{ mapDbId: string; linkageGroupDbId: string }>();
+  const mapDbId = decodeURIComponent(params.mapDbId);
+  const linkageGroupDbId = decodeURIComponent(params.linkageGroupDbId);
+
+  const [loading, setLoading] = useState(true);
+  const [error, setError] = useState<string | null>(null);
+  const [mapDetail, setMapDetail] = useState<GenomeMapRecord | null>(null);
+  const [linkageGroup, setLinkageGroup] = useState<LinkageGroupRecord | null>(null);
+
+  const loadDetail = useCallback(async () => {
+    const [map, group] = await Promise.all([
+      fetchGenomeMapDetail(mapDbId),
+      fetchLinkageGroupDetail(mapDbId, linkageGroupDbId),
+    ]);
+    if (!group) throw new Error("连锁群不存在");
+    setMapDetail(map);
+    setLinkageGroup(group);
+  }, [mapDbId, linkageGroupDbId]);
+
+  useEffect(() => {
+    let mounted = true;
+    setLoading(true);
+    setError(null);
+    loadDetail()
+      .catch((event) => {
+        if (!mounted) return;
+        setError(event instanceof Error ? event.message : "加载连锁群详情失败");
+      })
+      .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 || !linkageGroup || !mapDetail) {
+    return (
+      <div className="rounded-xl border border-destructive/20 bg-destructive/10 px-4 py-6 text-sm text-destructive">
+        {error || "连锁群不存在"}
+        <div className="mt-4">
+          <Button asChild variant="outline">
+            <Link href="/genotyping/genome-map?tab=linkage-groups">
+              <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/genome-map/maps/${encodeURIComponent(mapDbId)}`}>
+          <ArrowLeft className="mr-2 h-4 w-4" />
+          返回图谱详情
+        </Link>
+      </Button>
+
+      <Card>
+        <CardHeader className="pb-3">
+          <CardTitle className="flex items-center gap-2 text-lg">
+            <GitBranch className="h-5 w-5 text-emerald-500" />
+            {linkageGroup.linkage_group_name || linkageGroup.id}
+          </CardTitle>
+        </CardHeader>
+        <CardContent className="grid gap-3 text-sm sm:grid-cols-2 lg:grid-cols-4">
+          <div><span className="text-slate-500">LinkageGroup ID：</span>{linkageGroup.id}</div>
+          <div>
+            <span className="text-slate-500">所属图谱：</span>
+            <Link
+              href={`/genotyping/genome-map/maps/${encodeURIComponent(mapDbId)}`}
+              className="text-teal-600 hover:underline dark:text-teal-400"
+            >
+              {mapDetail.map_name || mapDbId}
+            </Link>
+          </div>
+          <div><span className="text-slate-500">最大位置：</span>{linkageGroup.max_position ?? "—"}</div>
+          <div className="flex items-center gap-2">
+            <span className="text-slate-500">Marker 数：</span>
+            <Badge variant="outline">{linkageGroup.marker_count ?? 0}</Badge>
+          </div>
+        </CardContent>
+      </Card>
+
+      <div className="flex flex-wrap gap-2">
+        <Button asChild variant="outline" size="sm">
+          <Link href={`/genotyping/genome-map?tab=marker-positions&map_db_id=${encodeURIComponent(mapDbId)}&linkage_group_name=${encodeURIComponent(linkageGroup.linkage_group_name || "")}`}>
+            <Map className="mr-2 h-4 w-4" />
+            在 Marker Position 列表中查看
+          </Link>
+        </Button>
+      </div>
+
+      <MarkerPositionEntityPage
+        mapDbId={mapDbId}
+        linkageGroupDbId={linkageGroupDbId}
+        linkageGroupName={linkageGroup.linkage_group_name}
+        onChanged={loadDetail}
+        defaultFormValues={{ linkage_group_id: linkageGroupDbId }}
+      />
+    </div>
+  );
+}

frontend/src/app/(app)/genotyping/genome-map/maps/[mapDbId]/page.tsx

@@ -0,0 +1,123 @@
+"use client";
+
+import Link from "next/link";
+import { useCallback, useEffect, useState } from "react";
+import { useParams } from "next/navigation";
+import { ArrowLeft, GitBranch, Map, Sigma } from "lucide-react";
+import { Button } from "@/components/ui/button";
+import { Card, CardContent, CardHeader, CardTitle } from "@/components/ui/card";
+import { Skeleton } from "@/components/ui/skeleton";
+import { LinkageGroupPanel } from "../../components/LinkageGroupPanel";
+import { MarkerPositionPanel } from "../../components/MarkerPositionPanel";
+import { fetchGenomeMapDetail } from "../../api";
+import { formatPublishedDate } from "../../genomeMapUtils";
+import type { GenomeMapDetail } from "../../types";
+
+export default function GenomeMapDetailPage() {
+  const params = useParams<{ mapDbId: string }>();
+  const mapDbId = decodeURIComponent(params.mapDbId);
+
+  const [loading, setLoading] = useState(true);
+  const [error, setError] = useState<string | null>(null);
+  const [detail, setDetail] = useState<GenomeMapDetail | null>(null);
+
+  const loadDetail = useCallback(async () => {
+    const record = await fetchGenomeMapDetail(mapDbId);
+    setDetail(record);
+  }, [mapDbId]);
+
+  useEffect(() => {
+    let mounted = true;
+    setLoading(true);
+    setError(null);
+    loadDetail()
+      .catch((event) => {
+        if (!mounted) return;
+        setError(event instanceof Error ? event.message : "加载图谱详情失败");
+      })
+      .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 || "图谱不存在"}
+        <div className="mt-4">
+          <Button asChild variant="outline">
+            <Link href="/genotyping/genome-map"><ArrowLeft className="mr-2 h-4 w-4" />返回列表</Link>
+          </Button>
+        </div>
+      </div>
+    );
+  }
+
+  const hasDependencies = (detail.linkage_group_count ?? detail.linkageGroups.length) > 0
+    || (detail.marker_count ?? detail.markerPositions.length) > 0;
+
+  return (
+    <div className="flex min-h-full flex-col gap-4">
+      <Button asChild variant="outline" size="sm" className="w-fit">
+        <Link href="/genotyping/genome-map"><ArrowLeft className="mr-2 h-4 w-4" />返回 GenomeMap 列表</Link>
+      </Button>
+
+      <Card>
+        <CardHeader className="pb-3">
+          <CardTitle className="flex items-center gap-2 text-lg">
+            <Map className="h-5 w-5 text-teal-500" />
+            {detail.map_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">Map ID：</span>{detail.id}</div>
+          <div><span className="text-slate-500">作物：</span>{detail.common_crop_name || "—"}</div>
+          <div><span className="text-slate-500">类型：</span>{detail.type || "—"}</div>
+          <div><span className="text-slate-500">单位：</span>{detail.unit || "—"}</div>
+          <div><span className="text-slate-500">学名：</span>{detail.scientific_name || "—"}</div>
+          <div><span className="text-slate-500">Map PUI：</span>{detail.map_pui || "—"}</div>
+          <div><span className="text-slate-500">发表日期：</span>{formatPublishedDate(detail.published_date)}</div>
+          <div><span className="text-slate-500">连锁群数：</span>{detail.linkage_group_count ?? detail.linkageGroups.length}</div>
+          <div><span className="text-slate-500">Marker 数：</span>{detail.marker_count ?? detail.markerPositions.length}</div>
+          <div className="sm:col-span-2"><span className="text-slate-500">文档：</span>{detail.documentation_url || "—"}</div>
+          <div className="sm:col-span-2"><span className="text-slate-500">备注：</span>{detail.comments || "—"}</div>
+        </CardContent>
+      </Card>
+
+      {hasDependencies ? (
+        <p className="rounded-lg border border-amber-200 bg-amber-50 px-3 py-2 text-xs text-amber-800 dark:border-amber-900 dark:bg-amber-950 dark:text-amber-200">
+          删除图谱前请先移除下属连锁群与 Marker Position。
+        </p>
+      ) : null}
+
+      <div className="flex flex-wrap gap-2">
+        <Button asChild variant="outline" size="sm">
+          <Link href={`/genotyping/genome-map?tab=linkage-groups&map_db_id=${encodeURIComponent(detail.id)}`}>
+            <GitBranch className="mr-2 h-4 w-4" />
+            在 Linkage Group 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 管理
+          </Link>
+        </Button>
+      </div>
+
+      <LinkageGroupPanel mapDbId={mapDbId} onChanged={loadDetail} />
+      <MarkerPositionPanel mapDbId={mapDbId} onChanged={loadDetail} />
+    </div>
+  );
+}

frontend/src/app/(app)/genotyping/genome-map/page.tsx

@@ -0,0 +1,71 @@
+"use client";
+
+import { Suspense, useEffect, useState } from "react";
+import { useSearchParams } from "next/navigation";
+import { GitBranch, Map, MapPin } from "lucide-react";
+import { Tabs, TabsContent, TabsList, TabsTrigger } from "@/components/ui/tabs";
+import { Skeleton } from "@/components/ui/skeleton";
+import { GenomeMapTab } from "./components/GenomeMapTab";
+import { LinkageGroupTab } from "./components/LinkageGroupTab";
+import { MarkerPositionTab } from "./components/MarkerPositionTab";
+
+function GenomeMapPageContent() {
+  const searchParams = useSearchParams();
+  const [tab, setTab] = useState("genome-maps");
+
+  useEffect(() => {
+    const nextTab = searchParams.get("tab");
+    if (nextTab === "linkage-groups" || nextTab === "genome-maps" || nextTab === "marker-positions") {
+      setTab(nextTab);
+    }
+  }, [searchParams]);
+
+  return (
+    <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="genome-maps" className="gap-2">
+          <Map className="h-4 w-4" />
+          GenomeMap
+        </TabsTrigger>
+        <TabsTrigger value="linkage-groups" className="gap-2">
+          <GitBranch className="h-4 w-4" />
+          Linkage Group
+        </TabsTrigger>
+        <TabsTrigger value="marker-positions" className="gap-2">
+          <MapPin className="h-4 w-4" />
+          Marker Position
+        </TabsTrigger>
+      </TabsList>
+
+      {tab === "genome-maps" ? (
+        <TabsContent value="genome-maps" className="mt-0 min-h-0 flex-1">
+          <GenomeMapTab />
+        </TabsContent>
+      ) : null}
+
+      {tab === "linkage-groups" ? (
+        <TabsContent value="linkage-groups" className="mt-0 min-h-0 flex-1">
+          <LinkageGroupTab />
+        </TabsContent>
+      ) : null}
+
+      {tab === "marker-positions" ? (
+        <TabsContent value="marker-positions" className="mt-0 min-h-0 flex-1">
+          <MarkerPositionTab />
+        </TabsContent>
+      ) : null}
+    </Tabs>
+  );
+}
+
+function PageFallback() {
+  return <Skeleton className="h-96 w-full rounded-xl" />;
+}
+
+export default function GenomeMapPage() {
+  return (
+    <Suspense fallback={<PageFallback />}>
+      <GenomeMapPageContent />
+    </Suspense>
+  );
+}

frontend/src/app/(app)/genotyping/genome-map/types.ts

@@ -0,0 +1,84 @@
+export const NONE_SELECT_VALUE = "__none__";
+
+export type SelectOption = { value: string; label: string };
+
+export type GenomeMapQuery = {
+  map_name?: string;
+  common_crop_name?: string;
+  type?: string;
+};
+
+export type LinkageGroupQuery = {
+  linkage_group_name?: string;
+  map_db_id?: string;
+};
+
+export type MarkerPositionQuery = {
+  map_db_id?: string;
+  linkage_group_name?: string;
+  variant_db_id?: string;
+};
+
+export type GenomeMapRecord = {
+  id: string;
+  mapDbId?: string;
+  map_name?: string | null;
+  mapName?: string | null;
+  map_pui?: string | null;
+  mapPUI?: string | null;
+  common_crop_name?: string | null;
+  commonCropName?: string | null;
+  scientific_name?: string | null;
+  scientificName?: string | null;
+  type?: string | null;
+  unit?: string | null;
+  comments?: string | null;
+  documentation_url?: string | null;
+  documentationURL?: string | null;
+  published_date?: string | null;
+  publishedDate?: string | null;
+  linkage_group_count?: number | null;
+  linkageGroupCount?: number | null;
+  marker_count?: number | null;
+  markerCount?: number | null;
+};
+
+export type LinkageGroupRecord = {
+  id: string;
+  linkage_group_db_id?: string;
+  linkageGroupDbId?: string;
+  linkage_group_name?: string | null;
+  linkageGroupName?: string | null;
+  max_position?: number | null;
+  maxPosition?: number | null;
+  marker_count?: number | null;
+  markerCount?: number | null;
+  map_db_id?: string | null;
+  mapDbId?: string | null;
+  map_name?: string | null;
+  mapName?: string | null;
+};
+
+export type MarkerPositionRecord = {
+  id: string;
+  marker_position_db_id?: string;
+  markerPositionDbId?: string;
+  linkage_group_db_id?: string;
+  linkageGroupDbId?: string;
+  linkage_group_name?: string | null;
+  linkageGroupName?: string | null;
+  variant_db_id?: string | null;
+  variantDbId?: string | null;
+  variant_name?: string | null;
+  variantName?: string | null;
+  position?: number | null;
+  map_db_id?: string | null;
+  mapDbId?: string | null;
+  map_name?: string | null;
+  mapName?: string | null;
+};
+
+export type GenomeMapDetail = GenomeMapRecord & {
+  linkageGroups: LinkageGroupRecord[];
+  markerPositions: MarkerPositionRecord[];
+};

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

@@ -3,7 +3,9 @@ import { getAuthToken } from "@/utils/token";
 import {
   NONE_SELECT_VALUE,
   type SelectOption,
+  type VariantSetAnalysisItem,
   type VariantSetDetail,
+  type VariantSetFormatItem,
   type VariantSetQuery,
   type VariantSetRecord,
 } from "./types";
@@ -273,6 +275,184 @@ export async function deleteVariantSetRow(id: string): Promise<void> {
   invalidateVariantSetPageCache();
 }
 
+const mapAnalysisRow = (item: VariantSetAnalysisItem): VariantSetAnalysisItem => ({
+  ...item,
+  id: item.analysisDbId || item.id,
+  analysisName: item.analysisName ?? null,
+  type: item.type ?? null,
+  description: item.description ?? null,
+  software: Array.isArray(item.software)
+    ? item.software
+    : (item.software ? [String(item.software)] : []),
+  created: item.created ?? null,
+  updated: item.updated ?? null,
+});
+
+const mapFormatRow = (item: VariantSetFormatItem): VariantSetFormatItem => ({
+  ...item,
+  id: item.formatDbId || item.id,
+  dataFormat: item.dataFormat ?? item.data_format ?? null,
+  fileFormat: item.fileFormat ?? item.file_format ?? null,
+  fileURL: item.fileURL ?? item.fileurl ?? null,
+  expandHomozygotes: item.expandHomozygotes ?? item.expand_homozygotes ?? null,
+  sepPhased: item.sepPhased ?? item.sep_phased ?? null,
+  sepUnphased: item.sepUnphased ?? item.sep_unphased ?? null,
+  unknownString: item.unknownString ?? item.unknown_string ?? null,
+});
+
+const parseSoftwareLines = (value: unknown) => String(value ?? "")
+  .split(/\r?\n/)
+  .map((line) => line.trim())
+  .filter(Boolean);
+
+const isValidUrl = (value: string) => {
+  try {
+    const url = new URL(value);
+    return url.protocol === "http:" || url.protocol === "https:";
+  } catch {
+    return false;
+  }
+};
+
+const analysisBody = (payload: Partial<Record<string, unknown>>) => {
+  const analysisName = requiredText(payload.analysis_name, "分析名称不能为空");
+  const software = parseSoftwareLines(payload.software_text);
+  for (const item of software) {
+    if (item.startsWith("http") && !isValidUrl(item)) {
+      throw new Error(`Software URL 格式无效：${item}`);
+    }
+  }
+  return {
+    analysisDbId: optionalText(payload.id),
+    analysisName,
+    description: optionalText(payload.description),
+    type: optionalText(payload.type === NONE_SELECT_VALUE ? null : payload.type),
+    created: optionalText(payload.created),
+    updated: optionalText(payload.updated),
+    software,
+  };
+};
+
+const formatBody = (payload: Partial<Record<string, unknown>>) => {
+  const dataFormat = requiredText(payload.data_format, "请选择 data_format");
+  const fileFormat = requiredText(payload.file_format, "请选择 file_format");
+  const fileURL = optionalText(payload.fileurl);
+  if (fileURL && !isValidUrl(fileURL)) {
+    throw new Error("fileurl 格式无效，请输入 http(s) URL");
+  }
+  return {
+    formatDbId: optionalText(payload.id),
+    dataFormat,
+    fileFormat,
+    fileURL,
+    expandHomozygotes: payload.expand_homozygotes === true || payload.expand_homozygotes === "true",
+    sepPhased: optionalText(payload.sep_phased),
+    sepUnphased: optionalText(payload.sep_unphased),
+    unknownString: optionalText(payload.unknown_string),
+  };
+};
+
+export const normalizeVariantSetAnalysisFormData = (row: VariantSetAnalysisItem) => ({
+  id: row.id || row.analysisDbId || "",
+  analysis_name: row.analysisName || "",
+  type: row.type ? row.type : NONE_SELECT_VALUE,
+  description: row.description || "",
+  software_text: (Array.isArray(row.software) ? row.software : []).join("\n"),
+  created: row.created ? String(row.created).slice(0, 19) : "",
+  updated: row.updated ? String(row.updated).slice(0, 19) : "",
+});
+
+export const normalizeVariantSetFormatFormData = (row: VariantSetFormatItem) => ({
+  id: row.id || row.formatDbId || "",
+  data_format: row.dataFormat || NONE_SELECT_VALUE,
+  file_format: row.fileFormat || NONE_SELECT_VALUE,
+  fileurl: row.fileURL || "",
+  expand_homozygotes: row.expandHomozygotes === true,
+  sep_phased: row.sepPhased || "",
+  sep_unphased: row.sepUnphased || "",
+  unknown_string: row.unknownString || "",
+});
+
+export async function fetchVariantSetAnalysisRows(variantSetDbId: string): Promise<VariantSetAnalysisItem[]> {
+  const response = await request<BrapiListResponse<VariantSetAnalysisItem>>(
+    `/brapi/v2/variantsets/${encodeURIComponent(variantSetDbId)}/analysis`,
+  );
+  return response.result.data.map(mapAnalysisRow);
+}
+
+export async function fetchVariantSetFormatRows(variantSetDbId: string): Promise<VariantSetFormatItem[]> {
+  const response = await request<BrapiListResponse<VariantSetFormatItem>>(
+    `/brapi/v2/variantsets/${encodeURIComponent(variantSetDbId)}/availableformats`,
+  );
+  return response.result.data.map(mapFormatRow);
+}
+
+export async function createVariantSetAnalysisRow(
+  variantSetDbId: string,
+  payload: Partial<Record<string, unknown>>,
+): Promise<VariantSetAnalysisItem> {
+  const response = await request<BrapiListResponse<VariantSetAnalysisItem>>(
+    `/brapi/v2/variantsets/${encodeURIComponent(variantSetDbId)}/analysis`,
+    { method: "POST", body: JSON.stringify(analysisBody(payload)) },
+  );
+  invalidateVariantSetPageCache();
+  return mapAnalysisRow(response.result.data[0]);
+}
+
+export async function updateVariantSetAnalysisRow(
+  variantSetDbId: string,
+  id: string,
+  payload: Partial<Record<string, unknown>>,
+): Promise<VariantSetAnalysisItem> {
+  const response = await request<BrapiListResponse<VariantSetAnalysisItem>>(
+    `/brapi/v2/variantsets/${encodeURIComponent(variantSetDbId)}/analysis/${encodeURIComponent(id)}`,
+    { method: "PUT", body: JSON.stringify(analysisBody(payload)) },
+  );
+  invalidateVariantSetPageCache();
+  return mapAnalysisRow(response.result.data[0]);
+}
+
+export async function deleteVariantSetAnalysisRow(variantSetDbId: string, id: string): Promise<void> {
+  await request(
+    `/brapi/v2/variantsets/${encodeURIComponent(variantSetDbId)}/analysis/${encodeURIComponent(id)}`,
+    { method: "DELETE" },
+  );
+  invalidateVariantSetPageCache();
+}
+
+export async function createVariantSetFormatRow(
+  variantSetDbId: string,
+  payload: Partial<Record<string, unknown>>,
+): Promise<VariantSetFormatItem> {
+  const response = await request<BrapiListResponse<VariantSetFormatItem>>(
+    `/brapi/v2/variantsets/${encodeURIComponent(variantSetDbId)}/availableformats`,
+    { method: "POST", body: JSON.stringify(formatBody(payload)) },
+  );
+  invalidateVariantSetPageCache();
+  return mapFormatRow(response.result.data[0]);
+}
+
+export async function updateVariantSetFormatRow(
+  variantSetDbId: string,
+  id: string,
+  payload: Partial<Record<string, unknown>>,
+): Promise<VariantSetFormatItem> {
+  const response = await request<BrapiListResponse<VariantSetFormatItem>>(
+    `/brapi/v2/variantsets/${encodeURIComponent(variantSetDbId)}/availableformats/${encodeURIComponent(id)}`,
+    { method: "PUT", body: JSON.stringify(formatBody(payload)) },
+  );
+  invalidateVariantSetPageCache();
+  return mapFormatRow(response.result.data[0]);
+}
+
+export async function deleteVariantSetFormatRow(variantSetDbId: string, id: string): Promise<void> {
+  await request(
+    `/brapi/v2/variantsets/${encodeURIComponent(variantSetDbId)}/availableformats/${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([

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

@@ -0,0 +1,115 @@
+"use client";
+
+import { useCallback, useMemo } from "react";
+import { FlaskConical } from "lucide-react";
+import { BrapiEntityPage, type BrapiFormField } from "@/components/brapi/BrapiEntityPage";
+import { Label } from "@/components/ui/label";
+import { Textarea } from "@/components/ui/textarea";
+import {
+  createVariantSetAnalysisRow,
+  deleteVariantSetAnalysisRow,
+  fetchVariantSetAnalysisRows,
+  normalizeVariantSetAnalysisFormData,
+  updateVariantSetAnalysisRow,
+} from "../api";
+import { ANALYSIS_TYPE_OPTIONS, NONE_SELECT_VALUE } from "../types";
+
+interface VariantSetAnalysisPanelProps {
+  variantSetDbId: string;
+  onChanged?: () => void;
+}
+
+const optionOrNone = (label: string, options: readonly { value: string; label: string }[]) => [
+  { value: NONE_SELECT_VALUE, label },
+  ...options,
+];
+
+export function VariantSetAnalysisPanel({ variantSetDbId, onChanged }: VariantSetAnalysisPanelProps) {
+  const loadRows = useCallback(async () => {
+    const rows = await fetchVariantSetAnalysisRows(variantSetDbId);
+    return rows as unknown as Record<string, unknown>[];
+  }, [variantSetDbId]);
+
+  const findRowById = useCallback(async (id: string) => {
+    const rows = await fetchVariantSetAnalysisRows(variantSetDbId);
+    const row = rows.find((item) => item.id === id);
+    if (!row) throw new Error("Analysis 不存在");
+    return normalizeVariantSetAnalysisFormData(row);
+  }, [variantSetDbId]);
+
+  const wrapMutation = useCallback(<T,>(action: () => Promise<T>) => async () => {
+    const result = await action();
+    onChanged?.();
+    return result;
+  }, [onChanged]);
+
+  const fields = useMemo<BrapiFormField[]>(() => [
+    { key: "id", label: "Analysis ID", type: "text", placeholder: "留空则系统自动生成" },
+    { key: "analysis_name", label: "分析名称", type: "text", required: true, placeholder: "如 Standard QC" },
+    {
+      key: "type",
+      label: "分析类型",
+      type: "select",
+      options: optionOrNone("不指定类型", ANALYSIS_TYPE_OPTIONS),
+    },
+    { key: "description", label: "分析说明", type: "textarea", placeholder: "描述分析流程或 QC 标准" },
+    { key: "created", label: "创建时间", type: "text", placeholder: "2024-01-01T12:00:00+08:00" },
+    { key: "updated", label: "更新时间", type: "text", placeholder: "2024-01-01T12:00:00+08:00" },
+  ], []);
+
+  const columns = useMemo(() => [
+    { key: "analysisName", label: "分析名称" },
+    { key: "type", label: "类型" },
+    {
+      key: "software",
+      label: "Software",
+      render: (value: unknown) => {
+        if (Array.isArray(value)) return value.length ? value.join(", ") : "—";
+        return String(value ?? "—");
+      },
+    },
+    {
+      key: "description",
+      label: "说明",
+      render: (value: unknown) => {
+        const text = String(value ?? "");
+        if (!text) return "—";
+        return text.length > 40 ? `${text.slice(0, 40)}…` : text;
+      },
+    },
+  ], []);
+
+  return (
+    <BrapiEntityPage
+      useEnhancedDialog
+      icon={FlaskConical}
+      iconBg="bg-gradient-to-br from-amber-500 to-orange-600"
+      title="Analysis"
+      description="维护 VariantSet 的分析或 QC 信息，每条记录可关联多个 software（名称、版本或 URL）。"
+      addLabel="新增 Analysis"
+      columns={columns}
+      fields={fields}
+      data={[]}
+      loadData={loadRows}
+      fetchRecord={findRowById}
+      createRecord={(payload) => wrapMutation(() => createVariantSetAnalysisRow(variantSetDbId, payload))() as Promise<Record<string, unknown>>}
+      updateRecord={(id, payload) => wrapMutation(() => updateVariantSetAnalysisRow(variantSetDbId, id, payload))() as Promise<Record<string, unknown>>}
+      deleteRecord={(id) => wrapMutation(() => deleteVariantSetAnalysisRow(variantSetDbId, id))().then(() => undefined)}
+      renderFormExtra={({ formData, updateForm }) => (
+        <div className="col-span-2 space-y-1.5">
+          <Label htmlFor="software_text" className="text-xs text-slate-500">
+            Software 列表（每行一项，可为名称、版本或 URL）
+          </Label>
+          <Textarea
+            id="software_text"
+            value={String(formData.software_text ?? "")}
+            onChange={(event) => updateForm("software_text", event.target.value)}
+            placeholder={"GATK 4.5\nhttps://github.com/genotyping/QC"}
+            rows={4}
+          />
+          <p className="text-xs text-slate-500">若填写 URL，请使用 http(s) 格式。</p>
+        </div>
+      )}
+    />
+  );
+}

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

@@ -0,0 +1,132 @@
+"use client";
+
+import Link from "next/link";
+import { useCallback, useMemo } from "react";
+import { FileDown } from "lucide-react";
+import { BrapiEntityPage, type BrapiFormField } from "@/components/brapi/BrapiEntityPage";
+import { Label } from "@/components/ui/label";
+import { Switch } from "@/components/ui/switch";
+import {
+  createVariantSetFormatRow,
+  deleteVariantSetFormatRow,
+  fetchVariantSetFormatRows,
+  normalizeVariantSetFormatFormData,
+  updateVariantSetFormatRow,
+} from "../api";
+import { DATA_FORMAT_OPTIONS, FILE_FORMAT_OPTIONS, NONE_SELECT_VALUE } from "../types";
+
+interface VariantSetFormatPanelProps {
+  variantSetDbId: string;
+  onChanged?: () => void;
+}
+
+const optionOrNone = (label: string, options: readonly { value: string; label: string }[]) => [
+  { value: NONE_SELECT_VALUE, label },
+  ...options,
+];
+
+const boolLabel = (value: unknown) => (value === true ? "是" : value === false ? "否" : "—");
+
+export function VariantSetFormatPanel({ variantSetDbId, onChanged }: VariantSetFormatPanelProps) {
+  const loadRows = useCallback(async () => {
+    const rows = await fetchVariantSetFormatRows(variantSetDbId);
+    return rows as unknown as Record<string, unknown>[];
+  }, [variantSetDbId]);
+
+  const findRowById = useCallback(async (id: string) => {
+    const rows = await fetchVariantSetFormatRows(variantSetDbId);
+    const row = rows.find((item) => item.id === id);
+    if (!row) throw new Error("Available Format 不存在");
+    return normalizeVariantSetFormatFormData(row);
+  }, [variantSetDbId]);
+
+  const wrapMutation = useCallback(<T,>(action: () => Promise<T>) => async () => {
+    const result = await action();
+    onChanged?.();
+    return result;
+  }, [onChanged]);
+
+  const fields = useMemo<BrapiFormField[]>(() => [
+    { key: "id", label: "Format ID", type: "text", placeholder: "留空则系统自动生成" },
+    {
+      key: "data_format",
+      label: "数据格式 (data_format)",
+      type: "select",
+      required: true,
+      options: optionOrNone("请选择数据格式", DATA_FORMAT_OPTIONS),
+    },
+    {
+      key: "file_format",
+      label: "文件格式 (file_format)",
+      type: "select",
+      required: true,
+      options: optionOrNone("请选择 MIME 类型", FILE_FORMAT_OPTIONS),
+    },
+    { key: "fileurl", label: "文件 URL (fileurl)", type: "text", placeholder: "https://example.com/data.vcf" },
+    { key: "sep_phased", label: "Phased 分隔符", type: "text", placeholder: "如 |" },
+    { key: "sep_unphased", label: "Unphased 分隔符", type: "text", placeholder: "如 /" },
+    { key: "unknown_string", label: "缺失值字符串", type: "text", placeholder: "如 NA 或 ." },
+  ], []);
+
+  const columns = useMemo(() => [
+    { key: "dataFormat", label: "数据格式" },
+    { key: "fileFormat", label: "MIME" },
+    {
+      key: "fileURL",
+      label: "文件 URL",
+      render: (value: unknown) => {
+        const url = String(value ?? "").trim();
+        if (!url) return "—";
+        return (
+          <Link href={url} target="_blank" rel="noopener noreferrer" className="break-all text-violet-600 hover:underline dark:text-violet-400">
+            {url}
+          </Link>
+        );
+      },
+    },
+    {
+      key: "expandHomozygotes",
+      label: "展开纯合",
+      render: (value: unknown) => boolLabel(value),
+    },
+    { key: "sepPhased", label: "Phased 分隔符" },
+    { key: "sepUnphased", label: "Unphased 分隔符" },
+    { key: "unknownString", label: "缺失值" },
+  ], []);
+
+  return (
+    <BrapiEntityPage
+      useEnhancedDialog
+      icon={FileDown}
+      iconBg="bg-gradient-to-br from-sky-500 to-blue-600"
+      title="Available Formats"
+      description="配置 VariantSet 可下载的数据格式与文件地址；矩阵格式可设置分隔符与缺失值字符串。"
+      addLabel="新增 Format"
+      columns={columns}
+      fields={fields}
+      data={[]}
+      loadData={loadRows}
+      fetchRecord={findRowById}
+      createRecord={(payload) => wrapMutation(() => createVariantSetFormatRow(variantSetDbId, payload))() as Promise<Record<string, unknown>>}
+      updateRecord={(id, payload) => wrapMutation(() => updateVariantSetFormatRow(variantSetDbId, id, payload))() as Promise<Record<string, unknown>>}
+      deleteRecord={(id) => wrapMutation(() => deleteVariantSetFormatRow(variantSetDbId, id))().then(() => undefined)}
+      renderFormExtra={({ formData, updateFormBatch }) => (
+        <div className="col-span-2 flex items-center justify-between rounded-lg border border-sky-100 bg-sky-50/60 p-3 dark:border-sky-900/40 dark:bg-sky-950/30">
+          <div>
+            <Label htmlFor="expand_homozygotes" className="text-sm font-medium text-sky-900 dark:text-sky-100">
+              展开纯合位点 (expand_homozygotes)
+            </Label>
+            <p className="mt-1 text-xs text-sky-800/80 dark:text-sky-200/80">
+              矩阵格式导入时会按此设置解析 phased / unphased 与缺失值。
+            </p>
+          </div>
+          <Switch
+            id="expand_homozygotes"
+            checked={formData.expand_homozygotes === true}
+            onCheckedChange={(checked) => updateFormBatch({ expand_homozygotes: checked })}
+          />
+        </div>
+      )}
+    />
+  );
+}

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

@@ -11,17 +11,60 @@ export interface VariantSetQuery {
   study_id?: string;
 }
 
+export const DATA_FORMAT_OPTIONS = [
+  { value: "DartSeq", label: "DartSeq" },
+  { value: "VCF", label: "VCF" },
+  { value: "Hapmap", label: "Hapmap" },
+  { value: "tabular", label: "tabular" },
+  { value: "JSON", label: "JSON" },
+] as const;
+
+export const FILE_FORMAT_OPTIONS = [
+  { value: "application/json", label: "application/json" },
+  { value: "text/csv", label: "text/csv" },
+  { value: "text/tsv", label: "text/tsv" },
+  { value: "application/flapjack", label: "application/flapjack" },
+  { value: "application/excel", label: "application/excel" },
+  { value: "application/zip", label: "application/zip" },
+] as const;
+
+export const ANALYSIS_TYPE_OPTIONS = [
+  { value: "QC", label: "QC" },
+  { value: "Annotation", label: "Annotation" },
+  { value: "Filtering", label: "Filtering" },
+  { value: "Imputation", label: "Imputation" },
+] as const;
+
 export interface VariantSetAnalysisItem {
+  id?: string;
   analysisDbId?: string;
   analysisName?: string | null;
   type?: string | null;
-  software?: string | null;
+  description?: string | null;
+  software?: string[] | string | null;
+  created?: string | null;
+  updated?: string | null;
 }
 
 export interface VariantSetFormatItem {
+  id?: string;
+  formatDbId?: string;
+  variant_set_id?: string;
+  variantSetDbId?: string;
   dataFormat?: string | null;
+  data_format?: string | null;
   fileFormat?: string | null;
+  file_format?: string | null;
   fileURL?: string | null;
+  fileurl?: string | null;
+  expandHomozygotes?: boolean | null;
+  expand_homozygotes?: boolean | null;
+  sepPhased?: string | null;
+  sep_phased?: string | null;
+  sepUnphased?: string | null;
+  sep_unphased?: string | null;
+  unknownString?: string | null;
+  unknown_string?: string | null;
 }
 
 export interface VariantSetRecord {

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

@@ -3,12 +3,15 @@
 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 { ArrowLeft, Binary, FileDown, FlaskConical, 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 { Tabs, TabsContent, TabsList, TabsTrigger } from "@/components/ui/tabs";
+import { VariantSetAnalysisPanel } from "../../components/VariantSetAnalysisPanel";
+import { VariantSetFormatPanel } from "../../components/VariantSetFormatPanel";
 import {
   fetchVariantSetCallsets,
   fetchVariantSetDetail,
@@ -105,9 +108,28 @@ export default function VariantSetDetailPage() {
           <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>
+          <div><span className="text-slate-500">Analysis 数：</span>{detail.analysis_count ?? 0}</div>
+          <div><span className="text-slate-500">Formats 数：</span>{detail.format_count ?? 0}</div>
         </CardContent>
       </Card>
 
+      <Tabs defaultValue="overview" className="space-y-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="overview" className="gap-2">
+            <Sigma className="h-4 w-4" />
+            概览
+          </TabsTrigger>
+          <TabsTrigger value="analysis" className="gap-2">
+            <FlaskConical className="h-4 w-4" />
+            Analysis
+          </TabsTrigger>
+          <TabsTrigger value="formats" className="gap-2">
+            <FileDown className="h-4 w-4" />
+            Formats
+          </TabsTrigger>
+        </TabsList>
+
+        <TabsContent value="overview" className="space-y-4">
           <Card>
             <CardHeader className="pb-3">
               <CardTitle className="flex items-center gap-2 text-base">
@@ -190,44 +212,16 @@ export default function VariantSetDetailPage() {
               )}
             </CardContent>
           </Card>
+        </TabsContent>
 
-      <div className="grid gap-4 lg:grid-cols-2">
+        <TabsContent value="analysis">
-        <Card>
+          <VariantSetAnalysisPanel variantSetDbId={variantSetDbId} onChanged={loadDetail} />
-          <CardHeader className="pb-3">
+        </TabsContent>
-            <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>
+        <TabsContent value="formats">
-          <CardHeader className="pb-3">
+          <VariantSetFormatPanel variantSetDbId={variantSetDbId} onChanged={loadDetail} />
-            <CardTitle className="text-base">Available Formats</CardTitle>
+        </TabsContent>
-          </CardHeader>
+      </Tabs>
-          <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 +1,8 @@
 import { createCachedLoader } from "@/services/dropdownCache";
+import { DEFAULT_LIST_PAGE, DEFAULT_LIST_PAGE_SIZE } from "@/constants/api";
 import { getAuthToken } from "@/utils/token";
 import {
   NONE_SELECT_VALUE,
-  type CallRecord,
   type SelectOption,
   type VariantQuery,
   type VariantRecord,
@@ -46,13 +46,6 @@ interface VariantSetResponse {
   referenceSetDbId: string | null;
 }
 
-interface CallSetResponse {
-  callSetDbId: string;
-  callSetName: string | null;
-  sampleDbId: string | null;
-  sampleName: string | null;
-}
-
 type VariantPayload = Partial<Record<
   | "id"
   | "variant_name"
@@ -68,17 +61,6 @@ type VariantPayload = Partial<Record<
   unknown
 >>;
 
-type CallPayload = Partial<Record<
-  | "id"
-  | "call_set_id"
-  | "variant_id"
-  | "genotype_text"
-  | "genotype_likelihood"
-  | "read_depth"
-  | "phase_set",
-  unknown
->>;
-
 const apiBase = () => {
   if (typeof window !== "undefined") return "";
   return process.env.API_BASE_URL || process.env.NEXT_PUBLIC_API_BASE_URL || "http://localhost:8000";
@@ -127,16 +109,6 @@ const optionalBoolean = (value: unknown) => {
   return ["true", "1", "pass", "passed"].includes(normalized.toLowerCase());
 };
 
-const genotypeToText = (value: unknown) => {
-  if (!value) return null;
-  if (typeof value === "string") return value;
-  if (typeof value === "object" && "values" in value) {
-    const values = (value as { values?: unknown[] }).values;
-    return Array.isArray(values) ? values.map((item) => String(item)).join("/") : null;
-  }
-  return null;
-};
-
 export const mapVariant = (variant: VariantRecord): VariantRecord => ({
   ...variant,
   id: variant.variantDbId || variant.variantId || variant.id,
@@ -161,19 +133,6 @@ export const mapVariant = (variant: VariantRecord): VariantRecord => ({
   filters_passed: variant.filters_passed ?? variant.filtersPassed ?? null,
 });
 
-const mapCall = (call: CallRecord): CallRecord => ({
-  ...call,
-  id: call.callDbId || call.id,
-  call_set_id: call.call_set_id || call.callSetDbId || null,
-  call_set_name: call.call_set_name || call.callSetName || null,
-  variant_id: call.variant_id || call.variantDbId || null,
-  variant_name: call.variant_name || call.variantName || null,
-  genotype_text: call.genotype_text || call.genotypeText || genotypeToText(call.genotype),
-  genotype_likelihood: call.genotype_likelihood ?? call.genotypeLikelihood ?? null,
-  read_depth: call.read_depth ?? call.readDepth ?? null,
-  phase_set: call.phase_set || call.phaseSet || null,
-});
-
 const variantBody = (payload: VariantPayload) => ({
   variantName: requiredText(payload.variant_name, "Variant name is required"),
   variantType: optionalText(payload.variant_type),
@@ -187,15 +146,6 @@ const variantBody = (payload: VariantPayload) => ({
   filtersPassed: optionalBoolean(payload.filters_passed),
 });
 
-const callBody = (payload: CallPayload) => ({
-  callSetDbId: requiredText(payload.call_set_id, "CallSet is required"),
-  variantDbId: requiredText(payload.variant_id, "Variant is required"),
-  genotype: requiredText(payload.genotype_text, "Genotype is required"),
-  genotypeLikelihood: optionalNumber(payload.genotype_likelihood),
-  readDepth: optionalNumber(payload.read_depth),
-  phaseSet: optionalText(payload.phase_set),
-});
-
 export const normalizeVariantFormData = (row: VariantRecord) => ({
   id: row.id,
   variant_name: row.variant_name || "",
@@ -220,13 +170,11 @@ const variantSetLoader = createCachedLoader(async () => {
   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");
+  const response = await request<BrapiListResponse<VariantRecord>>("/brapi/v2/search/variants", {
+    method: "POST",
+    body: JSON.stringify({ page: DEFAULT_LIST_PAGE, pageSize: DEFAULT_LIST_PAGE_SIZE }),
+  });
   return response.result.data.map(mapVariant);
 });
 
@@ -264,8 +212,6 @@ function filterVariantRows(rows: VariantRecord[], query?: VariantQuery): Variant
 function buildVariantOptions(
   referenceSets: ReferenceSetResponse[],
   variantSets: VariantSetResponse[],
-  callSets: CallSetResponse[],
-  variants: VariantRecord[],
 ) {
   return {
     referenceSets: referenceSets.map((item) => ({
@@ -276,38 +222,25 @@ function buildVariantOptions(
       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([
+  const [referenceSets, variantSets] = await Promise.all([
     referenceSetLoader.load(force),
     variantSetLoader.load(force),
-    callSetLoader.load(force),
-    variantRowsLoader.load(force),
   ]);
 
-  return buildVariantOptions(referenceSets, variantSets, callSets, variants);
+  return buildVariantOptions(referenceSets, variantSets);
 }
 
 export async function fetchVariantRows(query?: VariantQuery): Promise<VariantRecord[]> {
@@ -324,7 +257,7 @@ export async function fetchVariantDetail(variantDbId: string): Promise<VariantRe
   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`),
+    request<BrapiListResponse<Record<string, never>>>(`/brapi/v2/variants/${encodeURIComponent(variantDbId)}/calls?pageSize=10`),
   ]);
 
   const mapped = mapVariant(detail.result);
@@ -339,11 +272,6 @@ export async function fetchVariantDetail(variantDbId: string): Promise<VariantRe
   };
 }
 
-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",
@@ -374,45 +302,17 @@ export async function deleteVariantRow(id: string): Promise<void> {
   invalidateVariantPageCache();
 }
 
-export async function createCallRow(payload: CallPayload): Promise<CallRecord> {
-  const response = await request<BrapiListResponse<CallRecord>>("/brapi/v2/calls", {
-    method: "POST",
-    body: JSON.stringify({
-      callDbId: requiredText(payload.id, "Call ID is required"),
-      ...callBody(payload),
-    }),
-  });
-  return mapCall(response.result.data[0]);
-}
-
-export async function updateCallRow(id: string, payload: CallPayload): Promise<CallRecord> {
-  const requestedId = optionalText(payload.id);
-  if (requestedId && requestedId !== id) throw new Error("Call ID is immutable. Create a new record instead.");
-  const response = await request<BrapiSingleResponse<CallRecord>>(`/brapi/v2/calls/${encodeURIComponent(id)}`, {
-    method: "PUT",
-    body: JSON.stringify(callBody(payload)),
-  });
-  return mapCall(response.result);
-}
-
-export async function deleteCallRow(id: string): Promise<void> {
-  await request<BrapiSingleResponse<CallRecord>>(`/brapi/v2/calls/${encodeURIComponent(id)}`, {
-    method: "DELETE",
-  });
-}
-
 export async function loadVariantPageData(options?: { query?: VariantQuery; force?: boolean }) {
   const force = options?.force ?? false;
-  const [referenceSets, variantSets, callSets, variants] = await Promise.all([
+  const [referenceSets, variantSets, 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),
+    options: buildVariantOptions(referenceSets, variantSets),
     rows: filterVariantRows(enrichedRows, options?.query),
   };
 }

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

@@ -0,0 +1,116 @@
+"use client";
+
+import Link from "next/link";
+import { useEffect, useState } from "react";
+import { MapPin } from "lucide-react";
+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 { fetchMarkerPositionsByVariantId } from "../../genome-map/api";
+import type { MarkerPositionRecord } from "../../genome-map/types";
+
+interface VariantMarkerPositionCardProps {
+  variantDbId: string;
+}
+
+export function VariantMarkerPositionCard({ variantDbId }: VariantMarkerPositionCardProps) {
+  const [loading, setLoading] = useState(true);
+  const [error, setError] = useState<string | null>(null);
+  const [rows, setRows] = useState<MarkerPositionRecord[]>([]);
+
+  useEffect(() => {
+    let mounted = true;
+    setLoading(true);
+    setError(null);
+    fetchMarkerPositionsByVariantId(variantDbId)
+      .then((result) => {
+        if (!mounted) return;
+        setRows(result);
+      })
+      .catch((event) => {
+        if (!mounted) return;
+        setError(event instanceof Error ? event.message : "加载 Marker Position 失败");
+      })
+      .finally(() => {
+        if (mounted) setLoading(false);
+      });
+    return () => { mounted = false; };
+  }, [variantDbId]);
+
+  return (
+    <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="space-y-3 text-sm">
+        {loading ? (
+          <Skeleton className="h-24 w-full" />
+        ) : error ? (
+          <p className="text-destructive">{error}</p>
+        ) : rows.length === 0 ? (
+          <p className="text-slate-600 dark:text-slate-300">
+            该 Variant 尚未关联遗传图谱位置。
+          </p>
+        ) : (
+          <div className="overflow-x-auto rounded-lg border border-slate-200 dark:border-slate-800">
+            <Table>
+              <TableHeader>
+                <TableRow>
+                  <TableHead>图谱</TableHead>
+                  <TableHead>连锁群</TableHead>
+                  <TableHead>位置</TableHead>
+                </TableRow>
+              </TableHeader>
+              <TableBody>
+                {rows.map((row) => (
+                  <TableRow key={row.id}>
+                    <TableCell>
+                      {row.map_db_id ? (
+                        <Link
+                          href={`/genotyping/genome-map/maps/${encodeURIComponent(row.map_db_id)}`}
+                          className="text-teal-600 hover:underline dark:text-teal-400"
+                        >
+                          {row.map_name || row.map_db_id}
+                        </Link>
+                      ) : "—"}
+                    </TableCell>
+                    <TableCell>
+                      {row.linkage_group_db_id && row.map_db_id ? (
+                        <Link
+                          href={`/genotyping/genome-map/maps/${encodeURIComponent(row.map_db_id)}/linkage-groups/${encodeURIComponent(row.linkage_group_db_id)}`}
+                          className="text-teal-600 hover:underline dark:text-teal-400"
+                        >
+                          {row.linkage_group_name || row.linkage_group_db_id}
+                        </Link>
+                      ) : (row.linkage_group_name || "—")}
+                    </TableCell>
+                    <TableCell>{row.position ?? "—"}</TableCell>
+                  </TableRow>
+                ))}
+              </TableBody>
+            </Table>
+          </div>
+        )}
+
+        <div className="flex flex-wrap gap-2">
+          <Button asChild variant="link" className="h-auto px-0 text-cyan-600 dark:text-cyan-400">
+            <Link href={`/genotyping/genome-map?tab=marker-positions&variant_db_id=${encodeURIComponent(variantDbId)}`}>
+              在 GenomeMap 模块维护 Marker Position
+            </Link>
+          </Button>
+        </div>
+      </CardContent>
+    </Card>
+  );
+}

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

@@ -1,106 +1,18 @@
 "use client";
 
-import { Suspense, useCallback, useMemo, useState } from "react";
+import { Suspense } from "react";
-import { Binary, Sigma } from "lucide-react";
+import { 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,
-  deleteCallRow,
-  fetchCallRows,
-  fetchVariantOptions,
-  updateCallRow,
-} from "./api";
-import { NONE_SELECT_VALUE, type SelectOption } from "./types";
 
 function VariantTabFallback() {
   return <Skeleton className="h-96 w-full rounded-xl" />;
 }
 
 export default function VariantPage() {
-  const [tab, setTab] = useState("variants");
-  const [callSetOptions, setCallSetOptions] = useState<SelectOption[]>([]);
-  const [variantOptions, setVariantOptions] = useState<SelectOption[]>([]);
-
-  const loadOptions = useCallback(async () => {
-    const options = await fetchVariantOptions();
-    setCallSetOptions(options.callSets);
-    setVariantOptions(options.variants);
-    return options;
-  }, []);
-
-  const loadCalls = useCallback(async () => {
-    const [, rows] = await Promise.all([loadOptions(), fetchCallRows()]);
-    return rows as unknown as Record<string, unknown>[];
-  }, [loadOptions]);
-
-  const callFields = useMemo<BrapiFormField[]>(() => [
-    { key: "id", label: "Call ID", type: "text", required: true, placeholder: "call-001" },
-    {
-      key: "call_set_id",
-      label: "CallSet",
-      type: "select",
-      required: true,
-      options: callSetOptions,
-    },
-    {
-      key: "variant_id",
-      label: "Variant",
-      type: "select",
-      required: true,
-      options: variantOptions,
-    },
-    { key: "genotype_text", label: "Genotype", type: "text", required: true, placeholder: "A/G" },
-    { key: "genotype_likelihood", label: "似然值", type: "number", placeholder: "0.98" },
-    { key: "read_depth", label: "测序深度", type: "number", placeholder: "42" },
-    { key: "phase_set", label: "Phase Set", type: "text", placeholder: "PS001" },
-  ], [callSetOptions, variantOptions]);
-
   return (
-    <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>
-
-      {tab === "variants" ? (
-        <TabsContent value="variants" className="mt-0 min-h-0 flex-1">
     <Suspense fallback={<VariantTabFallback />}>
       <VariantTab />
     </Suspense>
-        </TabsContent>
-      ) : null}
-
-      {tab === "calls" ? (
-        <TabsContent value="calls" className="mt-0 min-h-0 flex-1">
-          <BrapiEntityPage
-            useEnhancedDialog
-            icon={Binary}
-            iconBg="bg-gradient-to-br from-sky-500 to-cyan-600"
-            title="Call 基因型判读"
-            description="维护样品 CallSet 在指定 Variant 上的 genotype、深度和相位信息。"
-            addLabel="新增 Call"
-            columns={[
-              { key: "callDbId", label: "Call ID" },
-              { key: "call_set_name", label: "CallSet" },
-              { key: "variant_name", label: "Variant" },
-              { key: "genotype_text", label: "Genotype" },
-              { key: "genotype_likelihood", label: "似然值" },
-              { key: "read_depth", label: "深度" },
-              { key: "phase_set", label: "Phase Set" },
-            ]}
-            fields={callFields}
-            data={[]}
-            stats={[{ label: "/brapi/v2/calls", value: "BrAPI", className: "bg-sky-50 text-sky-700 dark:bg-sky-400/10 dark:text-sky-200" }]}
-            loadData={loadCalls}
-            createRecord={(payload) => createCallRow(payload) as unknown as Promise<Record<string, unknown>>}
-            updateRecord={(id, payload) => updateCallRow(id, payload) as unknown as Promise<Record<string, unknown>>}
-            deleteRecord={deleteCallRow}
-          />
-        </TabsContent>
-      ) : null}
-    </Tabs>
   );
 }

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

@@ -3,12 +3,13 @@
 import Link from "next/link";
 import { useEffect, useState } from "react";
 import { useParams } from "next/navigation";
-import { ArrowLeft, MapPin, Sigma } from "lucide-react";
+import { ArrowLeft, 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";
+import { VariantMarkerPositionCard } from "../../components/VariantMarkerPositionCard";
 
 const boolLabel = (value: boolean | null | undefined) => {
   if (value === true) return "是";
@@ -97,30 +98,19 @@ export default function VariantDetailPage() {
           <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>
+          {(detail.allele_call_count ?? 0) > 0 ? (
-      </Card>
+            <div className="sm:col-span-2">
-
+              <Button asChild variant="link" className="h-auto px-0 text-cyan-600 dark:text-cyan-400">
-      <Card>
+                <Link href={`/genotyping/call-set?tab=allele-calls&variant_id=${encodeURIComponent(detail.id)}`}>
-        <CardHeader className="pb-3">
+                  查看该位点下的 allele_call
-          <CardTitle className="flex items-center gap-2 text-base">
-            <MapPin className="h-4 w-4 text-emerald-500" />
-            Marker Position
-          </CardTitle>
-        </CardHeader>
-        <CardContent className="text-sm text-slate-600 dark:text-slate-300">
-          <p>
-            Marker Position 与遗传图谱 linkage group 关联，可在后续 Marker / GenomeMap 模块中维护。
-            当前 Variant 详情已展示 allele_call 引用数量，便于删除前校验。
-          </p>
-          {detail.variant_set_id ? (
-            <Button asChild variant="link" className="mt-2 h-auto px-0 text-violet-600 dark:text-violet-400">
-              <Link href={`/genotyping/variant-set/variant-sets/${encodeURIComponent(detail.variant_set_id)}`}>
-                查看所属 VariantSet
                 </Link>
               </Button>
+            </div>
           ) : null}
         </CardContent>
       </Card>
+
+      <VariantMarkerPositionCard variantDbId={detail.id} />
     </div>
   );
 }

frontend/src/components/brapi/BrapiEntityPage.tsx

@@ -158,6 +158,8 @@ export interface BrapiFormField {
   label: string;
   type: "text" | "select" | "date" | "number" | "textarea" | "year";
   required?: boolean;
+  /** 只读展示，用户不可编辑（如后端自动生成的字段） */
+  readOnly?: boolean;
   placeholder?: string;
   options?: Array<{ value: string; label: string }>;
   colSpan?: 1 | 2;
@@ -256,8 +258,14 @@ export function BrapiEntityPage({
     ?? row.referenceDbId
     ?? row.referenceBasesDbId
     ?? row.variantSetDbId
+    ?? row.callSetDbId
     ?? row.variantDbId
     ?? row.callDbId
+    ?? row.mapDbId
+    ?? row.linkageGroupDbId
+    ?? row.markerPositionDbId
+    ?? row.analysisDbId
+    ?? row.formatDbId
     ?? "",
   ), []);
 
@@ -464,7 +472,11 @@ export function BrapiEntityPage({
               required={field.required}
             />
           ) : field.type === "select" ? (
-            <Select value={String(formData[field.key] ?? "")} onValueChange={(value) => updateForm(field.key, value)}>
+            <Select
+              value={String(formData[field.key] ?? "")}
+              onValueChange={(value) => updateForm(field.key, value)}
+              disabled={field.readOnly}
+            >
               <SelectTrigger id={field.key}><SelectValue placeholder={field.placeholder ?? `请选择${field.label}`} /></SelectTrigger>
               <SelectContent
                 position="popper"
@@ -474,9 +486,27 @@ export function BrapiEntityPage({
               </SelectContent>
             </Select>
           ) : field.type === "textarea" ? (
-            <Textarea id={field.key} value={String(formData[field.key] ?? "")} onChange={(event) => updateForm(field.key, event.target.value)} placeholder={field.placeholder} rows={3} className="resize-none" />
+            <Textarea
+              id={field.key}
+              value={String(formData[field.key] ?? "")}
+              onChange={(event) => updateForm(field.key, event.target.value)}
+              placeholder={field.placeholder}
+              rows={3}
+              className="resize-none"
+              readOnly={field.readOnly}
+              disabled={field.readOnly}
+            />
           ) : (
-            <Input id={field.key} type={field.type === "number" ? "number" : "text"} value={String(formData[field.key] ?? "")} onChange={(event) => updateForm(field.key, event.target.value)} placeholder={field.placeholder} />
+            <Input
+              id={field.key}
+              type={field.type === "number" ? "number" : "text"}
+              value={String(formData[field.key] ?? "")}
+              onChange={(event) => updateForm(field.key, event.target.value)}
+              placeholder={field.placeholder}
+              readOnly={field.readOnly}
+              disabled={field.readOnly}
+              className={field.readOnly ? "bg-slate-50 text-slate-500 dark:bg-slate-900 dark:text-slate-400" : undefined}
+            />
           )}
         </div>
       ))}

frontend/src/components/brapi/navigation.ts

@@ -1,6 +1,7 @@
 import type { LucideIcon } from "lucide-react";
 import {
   BarChart3,
+  Binary,
   BookCheck,
   BookOpen,
   Briefcase,
@@ -31,6 +32,7 @@ import {
   List as ListIcon,
   PanelTop,
   CalendarClock,
+  Map,
 } from "lucide-react";
 
 export interface BrapiNavItem {
@@ -143,7 +145,14 @@ export const brapiNavSections: BrapiNavSection[] = [
         title: "变异数据",
         items: [
           { title: "VariantSet", href: "/genotyping/variant-set", icon: Layers },
-          { title: "Variant / Call", href: "/genotyping/variant", icon: Sigma },
+          { title: "Variant", href: "/genotyping/variant", icon: Sigma },
+          { title: "CallSet / allele_call", href: "/genotyping/call-set", icon: Binary },
+        ],
+      },
+      {
+        title: "遗传图谱",
+        items: [
+          { title: "GenomeMap / LinkageGroup", href: "/genotyping/genome-map", icon: Map },
         ],
       },
     ],

frontend/src/constants/api.ts

@@ -6,6 +6,12 @@ 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}`;
 
+/** BrAPI token 分页接口（如 GET /variants） */
+export const DEFAULT_TOKEN_PAGE_QUERY = "pageToken=0&pageSize=1000";
+
+/** BrAPI search 分页请求体默认值 */
+export const DEFAULT_SEARCH_PAGE_BODY = { page: DEFAULT_LIST_PAGE, pageSize: 1000 } as const;
+
 export function buildPageQuery(page = DEFAULT_LIST_PAGE, pageSize = DEFAULT_LIST_PAGE_SIZE): string {
   return `page=${page}&pageSize=${pageSize}`;
 }

frontend/src/constants/menu.ts

@@ -86,7 +86,11 @@ export const mockBackendMenus: BackendMenuResponse[] = [
       { 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: "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: [] },
+        { title: "Variant", path: "/genotyping/variant", menu_type: "menu", icon: "sigma", order_index: 2, children: [] },
+        { title: "CallSet / allele_call", path: "/genotyping/call-set", menu_type: "menu", icon: "binary", order_index: 3, children: [] },
+      ] },
+      { title: "遗传图谱", path: "/genotyping/genome-map-group", menu_type: "folder", icon: "map", order_index: 4, children: [
+        { title: "GenomeMap / LinkageGroup", path: "/genotyping/genome-map", menu_type: "menu", icon: "map", order_index: 1, children: [] },
       ] }
     ]
   },

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

@@ -0,0 +1,80 @@
+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.CallSetWriteRequest;
+import org.brapi.test.BrAPITestServer.service.geno.CallSetService;
+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.CallSet;
+import io.swagger.model.geno.CallSetResponse;
+import io.swagger.model.geno.CallSetsListResponse;
+import io.swagger.model.geno.CallSetsListResponseResult;
+import jakarta.servlet.http.HttpServletRequest;
+
+@RestController
+public class GenotypingCallSetWriteController extends BrAPIController {
+
+	private static final Logger log = LoggerFactory.getLogger(GenotypingCallSetWriteController.class);
+
+	private final CallSetService callSetService;
+	private final HttpServletRequest request;
+
+	@Autowired
+	public GenotypingCallSetWriteController(CallSetService callSetService, HttpServletRequest request) {
+		this.callSetService = callSetService;
+		this.request = request;
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/callsets", produces = { "application/json" }, consumes = {
+			"application/json" }, method = RequestMethod.POST)
+	public ResponseEntity<CallSetsListResponse> callSetsPost(@RequestBody CallSetWriteRequest body,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		CallSet data = callSetService.saveCallSet(body);
+		return responseOK(new CallSetsListResponse(), new CallSetsListResponseResult(), List.of(data));
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/callsets/{callSetDbId}", produces = { "application/json" }, consumes = {
+			"application/json" }, method = RequestMethod.PUT)
+	public ResponseEntity<CallSetResponse> callSetsCallSetDbIdPut(@PathVariable("callSetDbId") String callSetDbId,
+			@RequestBody CallSetWriteRequest body,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		CallSet data = callSetService.updateCallSet(callSetDbId, body);
+		return responseOK(new CallSetResponse(), data);
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/callsets/{callSetDbId}", produces = {
+			"application/json" }, method = RequestMethod.DELETE)
+	public ResponseEntity<CallSetResponse> callSetsCallSetDbIdDelete(@PathVariable("callSetDbId") String callSetDbId,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		CallSet data = callSetService.deleteCallSet(callSetDbId);
+		return responseOK(new CallSetResponse(), data);
+	}
+}

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

@@ -0,0 +1,105 @@
+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.CallWriteRequest;
+import org.brapi.test.BrAPITestServer.service.geno.CallService;
+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.Metadata;
+import io.swagger.model.geno.Call;
+import io.swagger.model.geno.CallsListResponse;
+import io.swagger.model.geno.CallsListResponseResult;
+import jakarta.servlet.http.HttpServletRequest;
+
+@RestController
+public class GenotypingCallWriteController extends BrAPIController {
+
+	private static final Logger log = LoggerFactory.getLogger(GenotypingCallWriteController.class);
+
+	private final CallService callService;
+	private final HttpServletRequest request;
+
+	@Autowired
+	public GenotypingCallWriteController(CallService callService, HttpServletRequest request) {
+		this.callService = callService;
+		this.request = request;
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/calls", produces = { "application/json" }, consumes = {
+			"application/json" }, method = RequestMethod.POST)
+	public ResponseEntity<CallsListResponse> callsPost(@RequestBody CallWriteRequest body,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		Call data = callService.saveCall(body);
+		Metadata metadata = generateEmptyMetadata();
+		CallsListResponseResult result = new CallsListResponseResult();
+		result.setData(List.of(data));
+		return responseOK(new CallsListResponse(), result, metadata);
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/calls/import", produces = { "application/json" }, consumes = {
+			"application/json" }, method = RequestMethod.POST)
+	public ResponseEntity<CallsListResponse> callsImportPost(@RequestBody List<CallWriteRequest> body,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		List<Call> data = callService.importCalls(body);
+		Metadata metadata = generateEmptyMetadata();
+		CallsListResponseResult result = new CallsListResponseResult();
+		result.setData(data);
+		return responseOK(new CallsListResponse(), result, metadata);
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/calls/{callDbId}", produces = { "application/json" }, consumes = {
+			"application/json" }, method = RequestMethod.PUT)
+	public ResponseEntity<CallsListResponse> callsCallDbIdPut(@PathVariable("callDbId") String callDbId,
+			@RequestBody CallWriteRequest body,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		Call data = callService.updateCall(callDbId, body);
+		Metadata metadata = generateEmptyMetadata();
+		CallsListResponseResult result = new CallsListResponseResult();
+		result.setData(List.of(data));
+		return responseOK(new CallsListResponse(), result, metadata);
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/calls/{callDbId}", produces = {
+			"application/json" }, method = RequestMethod.DELETE)
+	public ResponseEntity<CallsListResponse> callsCallDbIdDelete(@PathVariable("callDbId") String callDbId,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		Call data = callService.deleteCall(callDbId);
+		Metadata metadata = generateEmptyMetadata();
+		CallsListResponseResult result = new CallsListResponseResult();
+		result.setData(List.of(data));
+		return responseOK(new CallsListResponse(), result, metadata);
+	}
+}

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

@@ -0,0 +1,176 @@
+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.GenomeMapWriteRequest;
+import org.brapi.test.BrAPITestServer.model.dto.geno.LinkageGroupWriteRequest;
+import org.brapi.test.BrAPITestServer.model.dto.geno.MarkerPositionWriteRequest;
+import org.brapi.test.BrAPITestServer.service.geno.GenomeMapService;
+import org.brapi.test.BrAPITestServer.service.geno.MarkerPositionService;
+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.GenomeMap;
+import io.swagger.model.geno.GenomeMapListResponse;
+import io.swagger.model.geno.GenomeMapListResponseResult;
+import io.swagger.model.geno.GenomeMapSingleResponse;
+import io.swagger.model.geno.LinkageGroup;
+import io.swagger.model.geno.LinkageGroupListResponse;
+import io.swagger.model.geno.LinkageGroupListResponseResult;
+import io.swagger.model.geno.MarkerPosition;
+import io.swagger.model.geno.MarkerPositionsListResponse;
+import io.swagger.model.geno.MarkerPositionsListResponseResult;
+import jakarta.servlet.http.HttpServletRequest;
+
+@RestController
+public class GenotypingGenomeMapWriteController extends BrAPIController {
+
+	private static final Logger log = LoggerFactory.getLogger(GenotypingGenomeMapWriteController.class);
+
+	private final GenomeMapService genomeMapService;
+	private final MarkerPositionService markerPositionService;
+	private final HttpServletRequest request;
+
+	@Autowired
+	public GenotypingGenomeMapWriteController(GenomeMapService genomeMapService,
+			MarkerPositionService markerPositionService, HttpServletRequest request) {
+		this.genomeMapService = genomeMapService;
+		this.markerPositionService = markerPositionService;
+		this.request = request;
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/maps", produces = { "application/json" }, consumes = {
+			"application/json" }, method = RequestMethod.POST)
+	public ResponseEntity<GenomeMapListResponse> mapsPost(@RequestBody GenomeMapWriteRequest body,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		GenomeMap data = genomeMapService.saveMap(body);
+		return responseOK(new GenomeMapListResponse(), new GenomeMapListResponseResult(), List.of(data));
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/maps/{mapDbId}", produces = { "application/json" }, consumes = {
+			"application/json" }, method = RequestMethod.PUT)
+	public ResponseEntity<GenomeMapSingleResponse> mapsMapDbIdPut(@PathVariable("mapDbId") String mapDbId,
+			@RequestBody GenomeMapWriteRequest body,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		GenomeMap data = genomeMapService.updateMap(mapDbId, body);
+		return responseOK(new GenomeMapSingleResponse(), data);
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/maps/{mapDbId}", produces = { "application/json" }, method = RequestMethod.DELETE)
+	public ResponseEntity<GenomeMapSingleResponse> mapsMapDbIdDelete(@PathVariable("mapDbId") String mapDbId,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		GenomeMap data = genomeMapService.deleteMap(mapDbId);
+		return responseOK(new GenomeMapSingleResponse(), data);
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/maps/{mapDbId}/linkagegroups", produces = { "application/json" }, consumes = {
+			"application/json" }, method = RequestMethod.POST)
+	public ResponseEntity<LinkageGroupListResponse> mapsMapDbIdLinkagegroupsPost(
+			@PathVariable("mapDbId") String mapDbId, @RequestBody LinkageGroupWriteRequest body,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		LinkageGroup data = genomeMapService.saveLinkageGroup(mapDbId, body);
+		return responseOK(new LinkageGroupListResponse(), new LinkageGroupListResponseResult(), List.of(data));
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/maps/{mapDbId}/linkagegroups/{linkageGroupDbId}", produces = {
+			"application/json" }, consumes = { "application/json" }, method = RequestMethod.PUT)
+	public ResponseEntity<LinkageGroupListResponse> mapsMapDbIdLinkagegroupsLinkageGroupDbIdPut(
+			@PathVariable("mapDbId") String mapDbId, @PathVariable("linkageGroupDbId") String linkageGroupDbId,
+			@RequestBody LinkageGroupWriteRequest body,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		LinkageGroup data = genomeMapService.updateLinkageGroup(mapDbId, linkageGroupDbId, body);
+		return responseOK(new LinkageGroupListResponse(), new LinkageGroupListResponseResult(), List.of(data));
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/maps/{mapDbId}/linkagegroups/{linkageGroupDbId}", produces = {
+			"application/json" }, method = RequestMethod.DELETE)
+	public ResponseEntity<LinkageGroupListResponse> mapsMapDbIdLinkagegroupsLinkageGroupDbIdDelete(
+			@PathVariable("mapDbId") String mapDbId, @PathVariable("linkageGroupDbId") String linkageGroupDbId,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		LinkageGroup data = genomeMapService.deleteLinkageGroup(mapDbId, linkageGroupDbId);
+		return responseOK(new LinkageGroupListResponse(), new LinkageGroupListResponseResult(), List.of(data));
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/markerpositions", produces = { "application/json" }, consumes = {
+			"application/json" }, method = RequestMethod.POST)
+	public ResponseEntity<MarkerPositionsListResponse> markerpositionsPost(@RequestBody MarkerPositionWriteRequest body,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		MarkerPosition data = markerPositionService.saveMarkerPosition(body);
+		return responseOK(new MarkerPositionsListResponse(), new MarkerPositionsListResponseResult(), List.of(data));
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/markerpositions/{markerPositionDbId}", produces = { "application/json" }, consumes = {
+			"application/json" }, method = RequestMethod.PUT)
+	public ResponseEntity<MarkerPositionsListResponse> markerpositionsMarkerPositionDbIdPut(
+			@PathVariable("markerPositionDbId") String markerPositionDbId,
+			@RequestBody MarkerPositionWriteRequest body,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		MarkerPosition data = markerPositionService.updateMarkerPosition(markerPositionDbId, body);
+		return responseOK(new MarkerPositionsListResponse(), new MarkerPositionsListResponseResult(), List.of(data));
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/markerpositions/{markerPositionDbId}", produces = {
+			"application/json" }, method = RequestMethod.DELETE)
+	public ResponseEntity<MarkerPositionsListResponse> markerpositionsMarkerPositionDbIdDelete(
+			@PathVariable("markerPositionDbId") String markerPositionDbId,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		MarkerPosition data = markerPositionService.deleteMarkerPosition(markerPositionDbId);
+		return responseOK(new MarkerPositionsListResponse(), new MarkerPositionsListResponseResult(), List.of(data));
+	}
+}

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

@@ -4,9 +4,16 @@ 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.VariantSetAnalysisListResponse;
+import org.brapi.test.BrAPITestServer.model.dto.geno.VariantSetAnalysisWriteRequest;
+import org.brapi.test.BrAPITestServer.model.dto.geno.VariantSetAvailableFormatListResponse;
+import org.brapi.test.BrAPITestServer.model.dto.geno.VariantSetAvailableFormatRecord;
+import org.brapi.test.BrAPITestServer.model.dto.geno.VariantSetAvailableFormatWriteRequest;
 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.VariantSetAnalysisService;
+import org.brapi.test.BrAPITestServer.service.geno.VariantSetAvailableFormatService;
 import org.brapi.test.BrAPITestServer.service.geno.VariantSetService;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -20,6 +27,7 @@ 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.Analysis;
 import io.swagger.model.geno.Variant;
 import io.swagger.model.geno.VariantSet;
 import io.swagger.model.geno.VariantSetResponse;
@@ -36,13 +44,19 @@ public class GenotypingVariantWriteController extends BrAPIController {
 	private static final Logger log = LoggerFactory.getLogger(GenotypingVariantWriteController.class);
 
 	private final VariantSetService variantSetService;
+	private final VariantSetAnalysisService variantSetAnalysisService;
+	private final VariantSetAvailableFormatService variantSetAvailableFormatService;
 	private final VariantService variantService;
 	private final HttpServletRequest request;
 
 	@Autowired
-	public GenotypingVariantWriteController(VariantSetService variantSetService, VariantService variantService,
+	public GenotypingVariantWriteController(VariantSetService variantSetService,
+			VariantSetAnalysisService variantSetAnalysisService,
+			VariantSetAvailableFormatService variantSetAvailableFormatService, VariantService variantService,
 			HttpServletRequest request) {
 		this.variantSetService = variantSetService;
+		this.variantSetAnalysisService = variantSetAnalysisService;
+		this.variantSetAvailableFormatService = variantSetAvailableFormatService;
 		this.variantService = variantService;
 		this.request = request;
 	}
@@ -88,6 +102,131 @@ public class GenotypingVariantWriteController extends BrAPIController {
 		return responseOK(new VariantSetResponse(), data);
 	}
 
+	@CrossOrigin
+	@RequestMapping(value = "/variantsets/{variantSetDbId}/analysis", produces = {
+			"application/json" }, method = RequestMethod.GET)
+	public ResponseEntity<VariantSetAnalysisListResponse> variantSetsVariantSetDbIdAnalysisGet(
+			@PathVariable("variantSetDbId") String variantSetDbId,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		List<Analysis> data = variantSetAnalysisService.findAnalysisByVariantSet(variantSetDbId);
+		return responseOK(new VariantSetAnalysisListResponse(), new VariantSetAnalysisListResponse.Result(), data);
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/variantsets/{variantSetDbId}/analysis", produces = { "application/json" }, consumes = {
+			"application/json" }, method = RequestMethod.POST)
+	public ResponseEntity<VariantSetAnalysisListResponse> variantSetsVariantSetDbIdAnalysisPost(
+			@PathVariable("variantSetDbId") String variantSetDbId, @RequestBody VariantSetAnalysisWriteRequest body,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		Analysis data = variantSetAnalysisService.saveAnalysis(variantSetDbId, body);
+		return responseOK(new VariantSetAnalysisListResponse(), new VariantSetAnalysisListResponse.Result(),
+				List.of(data));
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/variantsets/{variantSetDbId}/analysis/{analysisDbId}", produces = {
+			"application/json" }, consumes = { "application/json" }, method = RequestMethod.PUT)
+	public ResponseEntity<VariantSetAnalysisListResponse> variantSetsVariantSetDbIdAnalysisAnalysisDbIdPut(
+			@PathVariable("variantSetDbId") String variantSetDbId,
+			@PathVariable("analysisDbId") String analysisDbId, @RequestBody VariantSetAnalysisWriteRequest body,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		Analysis data = variantSetAnalysisService.updateAnalysis(variantSetDbId, analysisDbId, body);
+		return responseOK(new VariantSetAnalysisListResponse(), new VariantSetAnalysisListResponse.Result(),
+				List.of(data));
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/variantsets/{variantSetDbId}/analysis/{analysisDbId}", produces = {
+			"application/json" }, method = RequestMethod.DELETE)
+	public ResponseEntity<VariantSetAnalysisListResponse> variantSetsVariantSetDbIdAnalysisAnalysisDbIdDelete(
+			@PathVariable("variantSetDbId") String variantSetDbId,
+			@PathVariable("analysisDbId") String analysisDbId,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		Analysis data = variantSetAnalysisService.deleteAnalysis(variantSetDbId, analysisDbId);
+		return responseOK(new VariantSetAnalysisListResponse(), new VariantSetAnalysisListResponse.Result(),
+				List.of(data));
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/variantsets/{variantSetDbId}/availableformats", produces = {
+			"application/json" }, method = RequestMethod.GET)
+	public ResponseEntity<VariantSetAvailableFormatListResponse> variantSetsVariantSetDbIdAvailableformatsGet(
+			@PathVariable("variantSetDbId") String variantSetDbId,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		List<VariantSetAvailableFormatRecord> data = variantSetAvailableFormatService
+				.findFormatsByVariantSet(variantSetDbId);
+		return responseOK(new VariantSetAvailableFormatListResponse(),
+				new VariantSetAvailableFormatListResponse.Result(), data);
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/variantsets/{variantSetDbId}/availableformats", produces = { "application/json" },
+			consumes = { "application/json" }, method = RequestMethod.POST)
+	public ResponseEntity<VariantSetAvailableFormatListResponse> variantSetsVariantSetDbIdAvailableformatsPost(
+			@PathVariable("variantSetDbId") String variantSetDbId,
+			@RequestBody VariantSetAvailableFormatWriteRequest body,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		VariantSetAvailableFormatRecord data = variantSetAvailableFormatService.saveFormat(variantSetDbId, body);
+		return responseOK(new VariantSetAvailableFormatListResponse(),
+				new VariantSetAvailableFormatListResponse.Result(), List.of(data));
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/variantsets/{variantSetDbId}/availableformats/{formatDbId}", produces = {
+			"application/json" }, consumes = { "application/json" }, method = RequestMethod.PUT)
+	public ResponseEntity<VariantSetAvailableFormatListResponse> variantSetsVariantSetDbIdAvailableformatsFormatDbIdPut(
+			@PathVariable("variantSetDbId") String variantSetDbId, @PathVariable("formatDbId") String formatDbId,
+			@RequestBody VariantSetAvailableFormatWriteRequest body,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		VariantSetAvailableFormatRecord data = variantSetAvailableFormatService.updateFormat(variantSetDbId, formatDbId,
+				body);
+		return responseOK(new VariantSetAvailableFormatListResponse(),
+				new VariantSetAvailableFormatListResponse.Result(), List.of(data));
+	}
+
+	@CrossOrigin
+	@RequestMapping(value = "/variantsets/{variantSetDbId}/availableformats/{formatDbId}", produces = {
+			"application/json" }, method = RequestMethod.DELETE)
+	public ResponseEntity<VariantSetAvailableFormatListResponse> variantSetsVariantSetDbIdAvailableformatsFormatDbIdDelete(
+			@PathVariable("variantSetDbId") String variantSetDbId, @PathVariable("formatDbId") String formatDbId,
+			@RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException {
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_USER");
+		validateAcceptHeader(request);
+		VariantSetAvailableFormatRecord data = variantSetAvailableFormatService.deleteFormat(variantSetDbId, formatDbId);
+		return responseOK(new VariantSetAvailableFormatListResponse(),
+				new VariantSetAvailableFormatListResponse.Result(), List.of(data));
+	}
+
 	@CrossOrigin
 	@RequestMapping(value = "/variants", produces = { "application/json" }, consumes = {
 			"application/json" }, method = RequestMethod.POST)

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

@@ -0,0 +1,42 @@
+package org.brapi.test.BrAPITestServer.model.dto.geno;
+
+import java.util.List;
+
+public class CallSetWriteRequest {
+    private String callSetDbId;
+    private String callSetName;
+    private String sampleDbId;
+    private List<String> variantSetDbIds;
+
+    public String getCallSetDbId() {
+        return callSetDbId;
+    }
+
+    public void setCallSetDbId(String callSetDbId) {
+        this.callSetDbId = callSetDbId;
+    }
+
+    public String getCallSetName() {
+        return callSetName;
+    }
+
+    public void setCallSetName(String callSetName) {
+        this.callSetName = callSetName;
+    }
+
+    public String getSampleDbId() {
+        return sampleDbId;
+    }
+
+    public void setSampleDbId(String sampleDbId) {
+        this.sampleDbId = sampleDbId;
+    }
+
+    public List<String> getVariantSetDbIds() {
+        return variantSetDbIds;
+    }
+
+    public void setVariantSetDbIds(List<String> variantSetDbIds) {
+        this.variantSetDbIds = variantSetDbIds;
+    }
+}

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

@@ -0,0 +1,67 @@
+package org.brapi.test.BrAPITestServer.model.dto.geno;
+
+public class CallWriteRequest {
+    private String callDbId;
+    private String callSetDbId;
+    private String variantDbId;
+    private String genotype;
+    private Integer readDepth;
+    private Double genotypeLikelihood;
+    private String phaseSet;
+
+    public String getCallDbId() {
+        return callDbId;
+    }
+
+    public void setCallDbId(String callDbId) {
+        this.callDbId = callDbId;
+    }
+
+    public String getCallSetDbId() {
+        return callSetDbId;
+    }
+
+    public void setCallSetDbId(String callSetDbId) {
+        this.callSetDbId = callSetDbId;
+    }
+
+    public String getVariantDbId() {
+        return variantDbId;
+    }
+
+    public void setVariantDbId(String variantDbId) {
+        this.variantDbId = variantDbId;
+    }
+
+    public String getGenotype() {
+        return genotype;
+    }
+
+    public void setGenotype(String genotype) {
+        this.genotype = genotype;
+    }
+
+    public Integer getReadDepth() {
+        return readDepth;
+    }
+
+    public void setReadDepth(Integer readDepth) {
+        this.readDepth = readDepth;
+    }
+
+    public Double getGenotypeLikelihood() {
+        return genotypeLikelihood;
+    }
+
+    public void setGenotypeLikelihood(Double genotypeLikelihood) {
+        this.genotypeLikelihood = genotypeLikelihood;
+    }
+
+    public String getPhaseSet() {
+        return phaseSet;
+    }
+
+    public void setPhaseSet(String phaseSet) {
+        this.phaseSet = phaseSet;
+    }
+}

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

@@ -0,0 +1,94 @@
+package org.brapi.test.BrAPITestServer.model.dto.geno;
+
+public class GenomeMapWriteRequest {
+    private String mapDbId;
+    private String mapName;
+    private String mapPUI;
+    private String commonCropName;
+    private String scientificName;
+    private String type;
+    private String unit;
+    private String comments;
+    private String documentationURL;
+    private String publishedDate;
+
+    public String getMapDbId() {
+        return mapDbId;
+    }
+
+    public void setMapDbId(String mapDbId) {
+        this.mapDbId = mapDbId;
+    }
+
+    public String getMapName() {
+        return mapName;
+    }
+
+    public void setMapName(String mapName) {
+        this.mapName = mapName;
+    }
+
+    public String getMapPUI() {
+        return mapPUI;
+    }
+
+    public void setMapPUI(String mapPUI) {
+        this.mapPUI = mapPUI;
+    }
+
+    public String getCommonCropName() {
+        return commonCropName;
+    }
+
+    public void setCommonCropName(String commonCropName) {
+        this.commonCropName = commonCropName;
+    }
+
+    public String getScientificName() {
+        return scientificName;
+    }
+
+    public void setScientificName(String scientificName) {
+        this.scientificName = scientificName;
+    }
+
+    public String getType() {
+        return type;
+    }
+
+    public void setType(String type) {
+        this.type = type;
+    }
+
+    public String getUnit() {
+        return unit;
+    }
+
+    public void setUnit(String unit) {
+        this.unit = unit;
+    }
+
+    public String getComments() {
+        return comments;
+    }
+
+    public void setComments(String comments) {
+        this.comments = comments;
+    }
+
+    public String getDocumentationURL() {
+        return documentationURL;
+    }
+
+    public void setDocumentationURL(String documentationURL) {
+        this.documentationURL = documentationURL;
+    }
+
+    public String getPublishedDate() {
+        return publishedDate;
+    }
+
+    public void setPublishedDate(String publishedDate) {
+        this.publishedDate = publishedDate;
+    }
+}

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

@@ -0,0 +1,31 @@
+package org.brapi.test.BrAPITestServer.model.dto.geno;
+
+public class LinkageGroupWriteRequest {
+    private String linkageGroupDbId;
+    private String linkageGroupName;
+    private Integer maxPosition;
+
+    public String getLinkageGroupDbId() {
+        return linkageGroupDbId;
+    }
+
+    public void setLinkageGroupDbId(String linkageGroupDbId) {
+        this.linkageGroupDbId = linkageGroupDbId;
+    }
+
+    public String getLinkageGroupName() {
+        return linkageGroupName;
+    }
+
+    public void setLinkageGroupName(String linkageGroupName) {
+        this.linkageGroupName = linkageGroupName;
+    }
+
+    public Integer getMaxPosition() {
+        return maxPosition;
+    }
+
+    public void setMaxPosition(Integer maxPosition) {
+        this.maxPosition = maxPosition;
+    }
+}

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

@@ -0,0 +1,40 @@
+package org.brapi.test.BrAPITestServer.model.dto.geno;
+
+public class MarkerPositionWriteRequest {
+    private String markerPositionDbId;
+    private String linkageGroupDbId;
+    private String variantDbId;
+    private Integer position;
+
+    public String getMarkerPositionDbId() {
+        return markerPositionDbId;
+    }
+
+    public void setMarkerPositionDbId(String markerPositionDbId) {
+        this.markerPositionDbId = markerPositionDbId;
+    }
+
+    public String getLinkageGroupDbId() {
+        return linkageGroupDbId;
+    }
+
+    public void setLinkageGroupDbId(String linkageGroupDbId) {
+        this.linkageGroupDbId = linkageGroupDbId;
+    }
+
+    public String getVariantDbId() {
+        return variantDbId;
+    }
+
+    public void setVariantDbId(String variantDbId) {
+        this.variantDbId = variantDbId;
+    }
+
+    public Integer getPosition() {
+        return position;
+    }
+
+    public void setPosition(Integer position) {
+        this.position = position;
+    }
+}

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

@@ -0,0 +1,54 @@
+package org.brapi.test.BrAPITestServer.model.dto.geno;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import io.swagger.model.BrAPIResponse;
+import io.swagger.model.BrAPIResponseResult;
+import io.swagger.model.Context;
+import io.swagger.model.Metadata;
+import io.swagger.model.geno.Analysis;
+
+public class VariantSetAnalysisListResponse implements BrAPIResponse<VariantSetAnalysisListResponse.Result> {
+	private Context _atContext;
+	private Metadata metadata;
+	private Result result = new Result();
+
+	public static class Result implements BrAPIResponseResult<Analysis> {
+		private List<Analysis> data = new ArrayList<>();
+
+		@Override
+		public List<Analysis> getData() {
+			return data;
+		}
+
+		@Override
+		public void setData(List<Analysis> data) {
+			this.data = data;
+		}
+	}
+
+	public void set_atContext(Context _atContext) {
+		this._atContext = _atContext;
+	}
+
+	@Override
+	public Metadata getMetadata() {
+		return metadata;
+	}
+
+	@Override
+	public void setMetadata(Metadata metadata) {
+		this.metadata = metadata;
+	}
+
+	@Override
+	public Result getResult() {
+		return result;
+	}
+
+	@Override
+	public void setResult(Result result) {
+		this.result = result;
+	}
+}

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

@@ -0,0 +1,78 @@
+package org.brapi.test.BrAPITestServer.model.dto.geno;
+
+import java.util.List;
+
+public class VariantSetAnalysisWriteRequest {
+	private String analysisDbId;
+	private String variantSetDbId;
+	private String analysisName;
+	private String description;
+	private String type;
+	private String created;
+	private String updated;
+	private List<String> software;
+
+	public String getAnalysisDbId() {
+		return analysisDbId;
+	}
+
+	public void setAnalysisDbId(String analysisDbId) {
+		this.analysisDbId = analysisDbId;
+	}
+
+	public String getVariantSetDbId() {
+		return variantSetDbId;
+	}
+
+	public void setVariantSetDbId(String variantSetDbId) {
+		this.variantSetDbId = variantSetDbId;
+	}
+
+	public String getAnalysisName() {
+		return analysisName;
+	}
+
+	public void setAnalysisName(String analysisName) {
+		this.analysisName = analysisName;
+	}
+
+	public String getDescription() {
+		return description;
+	}
+
+	public void setDescription(String description) {
+		this.description = description;
+	}
+
+	public String getType() {
+		return type;
+	}
+
+	public void setType(String type) {
+		this.type = type;
+	}
+
+	public String getCreated() {
+		return created;
+	}
+
+	public void setCreated(String created) {
+		this.created = created;
+	}
+
+	public String getUpdated() {
+		return updated;
+	}
+
+	public void setUpdated(String updated) {
+		this.updated = updated;
+	}
+
+	public List<String> getSoftware() {
+		return software;
+	}
+
+	public void setSoftware(List<String> software) {
+		this.software = software;
+	}
+}

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

@@ -0,0 +1,55 @@
+package org.brapi.test.BrAPITestServer.model.dto.geno;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import io.swagger.model.BrAPIResponse;
+import io.swagger.model.BrAPIResponseResult;
+import io.swagger.model.Context;
+import io.swagger.model.Metadata;
+
+public class VariantSetAvailableFormatListResponse
+		implements BrAPIResponse<VariantSetAvailableFormatListResponse.Result> {
+	private Context _atContext;
+	private Metadata metadata;
+	private Result result = new Result();
+
+	public static class Result implements BrAPIResponseResult<VariantSetAvailableFormatRecord> {
+		private List<VariantSetAvailableFormatRecord> data = new ArrayList<>();
+
+		@Override
+		public List<VariantSetAvailableFormatRecord> getData() {
+			return data;
+		}
+
+		@Override
+		public void setData(List<VariantSetAvailableFormatRecord> data) {
+			this.data = data;
+		}
+	}
+
+	@Override
+	public void set_atContext(Context _atContext) {
+		this._atContext = _atContext;
+	}
+
+	@Override
+	public Metadata getMetadata() {
+		return metadata;
+	}
+
+	@Override
+	public void setMetadata(Metadata metadata) {
+		this.metadata = metadata;
+	}
+
+	@Override
+	public Result getResult() {
+		return result;
+	}
+
+	@Override
+	public void setResult(Result result) {
+		this.result = result;
+	}
+}

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

@@ -0,0 +1,85 @@
+package org.brapi.test.BrAPITestServer.model.dto.geno;
+
+public class VariantSetAvailableFormatRecord {
+	private String formatDbId;
+	private String variantSetDbId;
+	private String dataFormat;
+	private String fileFormat;
+	private String fileURL;
+	private Boolean expandHomozygotes;
+	private String sepPhased;
+	private String sepUnphased;
+	private String unknownString;
+
+	public String getFormatDbId() {
+		return formatDbId;
+	}
+
+	public void setFormatDbId(String formatDbId) {
+		this.formatDbId = formatDbId;
+	}
+
+	public String getVariantSetDbId() {
+		return variantSetDbId;
+	}
+
+	public void setVariantSetDbId(String variantSetDbId) {
+		this.variantSetDbId = variantSetDbId;
+	}
+
+	public String getDataFormat() {
+		return dataFormat;
+	}
+
+	public void setDataFormat(String dataFormat) {
+		this.dataFormat = dataFormat;
+	}
+
+	public String getFileFormat() {
+		return fileFormat;
+	}
+
+	public void setFileFormat(String fileFormat) {
+		this.fileFormat = fileFormat;
+	}
+
+	public String getFileURL() {
+		return fileURL;
+	}
+
+	public void setFileURL(String fileURL) {
+		this.fileURL = fileURL;
+	}
+
+	public Boolean getExpandHomozygotes() {
+		return expandHomozygotes;
+	}
+
+	public void setExpandHomozygotes(Boolean expandHomozygotes) {
+		this.expandHomozygotes = expandHomozygotes;
+	}
+
+	public String getSepPhased() {
+		return sepPhased;
+	}
+
+	public void setSepPhased(String sepPhased) {
+		this.sepPhased = sepPhased;
+	}
+
+	public String getSepUnphased() {
+		return sepUnphased;
+	}
+
+	public void setSepUnphased(String sepUnphased) {
+		this.sepUnphased = sepUnphased;
+	}
+
+	public String getUnknownString() {
+		return unknownString;
+	}
+
+	public void setUnknownString(String unknownString) {
+		this.unknownString = unknownString;
+	}
+}

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

@@ -0,0 +1,85 @@
+package org.brapi.test.BrAPITestServer.model.dto.geno;
+
+public class VariantSetAvailableFormatWriteRequest {
+	private String formatDbId;
+	private String variantSetDbId;
+	private String dataFormat;
+	private String fileFormat;
+	private String fileURL;
+	private Boolean expandHomozygotes;
+	private String sepPhased;
+	private String sepUnphased;
+	private String unknownString;
+
+	public String getFormatDbId() {
+		return formatDbId;
+	}
+
+	public void setFormatDbId(String formatDbId) {
+		this.formatDbId = formatDbId;
+	}
+
+	public String getVariantSetDbId() {
+		return variantSetDbId;
+	}
+
+	public void setVariantSetDbId(String variantSetDbId) {
+		this.variantSetDbId = variantSetDbId;
+	}
+
+	public String getDataFormat() {
+		return dataFormat;
+	}
+
+	public void setDataFormat(String dataFormat) {
+		this.dataFormat = dataFormat;
+	}
+
+	public String getFileFormat() {
+		return fileFormat;
+	}
+
+	public void setFileFormat(String fileFormat) {
+		this.fileFormat = fileFormat;
+	}
+
+	public String getFileURL() {
+		return fileURL;
+	}
+
+	public void setFileURL(String fileURL) {
+		this.fileURL = fileURL;
+	}
+
+	public Boolean getExpandHomozygotes() {
+		return expandHomozygotes;
+	}
+
+	public void setExpandHomozygotes(Boolean expandHomozygotes) {
+		this.expandHomozygotes = expandHomozygotes;
+	}
+
+	public String getSepPhased() {
+		return sepPhased;
+	}
+
+	public void setSepPhased(String sepPhased) {
+		this.sepPhased = sepPhased;
+	}
+
+	public String getSepUnphased() {
+		return sepUnphased;
+	}
+
+	public void setSepUnphased(String sepUnphased) {
+		this.sepUnphased = sepUnphased;
+	}
+
+	public String getUnknownString() {
+		return unknownString;
+	}
+
+	public void setUnknownString(String unknownString) {
+		this.unknownString = unknownString;
+	}
+}

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

@@ -2,6 +2,12 @@ package org.brapi.test.BrAPITestServer.repository.geno;
 
 import org.brapi.test.BrAPITestServer.model.entity.geno.CallEntity;
 import org.brapi.test.BrAPITestServer.repository.BrAPIRepository;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
 
 public interface CallRepository extends BrAPIRepository<CallEntity, String> {
+
+	@Query("SELECT COUNT(c) FROM CallEntity c WHERE c.callSet.id = :callSetDbId")
+	long countByCallSetDbId(@Param("callSetDbId") String callSetDbId);
+
 }

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

@@ -0,0 +1,10 @@
+package org.brapi.test.BrAPITestServer.repository.geno;
+
+import java.util.List;
+
+import org.brapi.test.BrAPITestServer.model.entity.geno.VariantSetAnalysisEntity;
+import org.springframework.data.jpa.repository.JpaRepository;
+
+public interface VariantSetAnalysisRepository extends JpaRepository<VariantSetAnalysisEntity, String> {
+	List<VariantSetAnalysisEntity> findByVariantSet_Id(String variantSetId);
+}

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

@@ -0,0 +1,10 @@
+package org.brapi.test.BrAPITestServer.repository.geno;
+
+import java.util.List;
+
+import org.brapi.test.BrAPITestServer.model.entity.geno.VariantSetAvailableFormatEntity;
+import org.springframework.data.jpa.repository.JpaRepository;
+
+public interface VariantSetAvailableFormatRepository extends JpaRepository<VariantSetAvailableFormatEntity, String> {
+	List<VariantSetAvailableFormatEntity> findByVariantSet_Id(String variantSetId);
+}

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

@@ -3,18 +3,27 @@ package org.brapi.test.BrAPITestServer.service.geno;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Optional;
+import java.util.Set;
 import java.util.stream.Collectors;
 
 import org.apache.commons.lang3.math.NumberUtils;
+import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerDbIdNotFoundException;
 import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerException;
+import org.brapi.test.BrAPITestServer.model.dto.geno.CallWriteRequest;
 import org.brapi.test.BrAPITestServer.model.entity.geno.CallEntity;
+import org.brapi.test.BrAPITestServer.model.entity.geno.CallSetEntity;
+import org.brapi.test.BrAPITestServer.model.entity.geno.VariantEntity;
 import org.brapi.test.BrAPITestServer.repository.geno.CallRepository;
 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.PageRequest;
 import org.springframework.data.domain.Pageable;
 import org.springframework.http.HttpStatus;
 import org.springframework.stereotype.Service;
@@ -37,9 +46,13 @@ public class CallService {
 	public static final String UNKNOWN_STRING_DEFAULT = ".";
 
 	private final CallRepository callRepository;
+	private final CallSetService callSetService;
+	private final VariantService variantService;
 
-	public CallService(CallRepository callRepository) {
+	public CallService(CallRepository callRepository, CallSetService callSetService, VariantService variantService) {
 		this.callRepository = callRepository;
+		this.callSetService = callSetService;
+		this.variantService = variantService;
 	}
 
 	public CallsListResponseResult findCalls(String callSetDbId, String variantDbId, String variantSetDbId,
@@ -103,7 +116,14 @@ public class CallService {
 
 	private Call convertFromEntityWithFormatting(CallEntity entity, CallsSearchRequest request) {
 		Call call = new Call();
-		call.setAdditionalInfo(entity.getAdditionalInfoMap());
+		Map<String, Object> additionalInfo = entity.getAdditionalInfoMap();
+		if (additionalInfo == null) {
+			additionalInfo = new HashMap<>();
+		} else {
+			additionalInfo = new HashMap<>(additionalInfo);
+		}
+		additionalInfo.put("callDbId", entity.getId());
+		call.setAdditionalInfo(additionalInfo);
 		if (entity.getCallSet() != null) {
 			call.setCallSetDbId(entity.getCallSet().getId());
 			call.setCallSetName(entity.getCallSet().getCallSetName());
@@ -154,6 +174,7 @@ public class CallService {
 	}
 
 	public CallsListResponseResult updateCalls(List<Call> body) throws BrAPIServerException {
+		ensureVariantSetBindings(body);
 		CallsSearchRequest searchReq = new CallsSearchRequest();
 		Map<String, Call> callsMap = new HashMap<>();
 		for (Call call : body) {
@@ -214,4 +235,126 @@ public class CallService {
 
 	}
 
+	public Call getCall(String callDbId) throws BrAPIServerException {
+		return convertFromEntity(getCallEntity(callDbId, HttpStatus.NOT_FOUND));
+	}
+
+	public CallEntity getCallEntity(String callDbId) throws BrAPIServerException {
+		return getCallEntity(callDbId, HttpStatus.BAD_REQUEST);
+	}
+
+	public CallEntity getCallEntity(String callDbId, HttpStatus errorStatus) throws BrAPIServerException {
+		Optional<CallEntity> entityOpt = callRepository.findById(callDbId);
+		if (entityOpt.isPresent()) {
+			return entityOpt.get();
+		}
+		throw new BrAPIServerDbIdNotFoundException("call", callDbId, errorStatus);
+	}
+
+	public Call saveCall(CallWriteRequest request) throws BrAPIServerException {
+		if (request.getCallSetDbId() == null || request.getCallSetDbId().isBlank()) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "callSetDbId is required");
+		}
+		if (request.getVariantDbId() == null || request.getVariantDbId().isBlank()) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "variantDbId is required");
+		}
+		if (request.getGenotype() == null || request.getGenotype().isBlank()) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "genotype is required");
+		}
+		if (request.getCallDbId() != null && callRepository.findById(request.getCallDbId()).isPresent()) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT, "Call already exists: " + request.getCallDbId());
+		}
+		CallSetEntity callSet = callSetService.getCallSetEntity(request.getCallSetDbId());
+		VariantEntity variant = variantService.getVariantEntity(request.getVariantDbId());
+		assertNoDuplicateCall(callSet.getId(), variant.getId(), null);
+		if (request.getReadDepth() != null && request.getReadDepth() < 0) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "readDepth cannot be negative");
+		}
+
+		CallEntity entity = new CallEntity();
+		if (request.getCallDbId() != null && !request.getCallDbId().isBlank()) {
+			entity.setId(request.getCallDbId().trim());
+		}
+		updateEntity(entity, request, callSet, variant);
+		Call saved = convertFromEntity(callRepository.save(entity));
+		if (variant.getVariantSet() != null) {
+			callSetService.ensureVariantSetBinding(callSet.getId(), variant.getVariantSet().getId());
+		}
+		return saved;
+	}
+
+	public List<Call> importCalls(List<CallWriteRequest> requests) throws BrAPIServerException {
+		List<Call> saved = new ArrayList<>();
+		for (CallWriteRequest request : requests) {
+			saved.add(saveCall(request));
+		}
+		return saved;
+	}
+
+	public Call updateCall(String callDbId, CallWriteRequest request) throws BrAPIServerException {
+		CallEntity entity = getCallEntity(callDbId, HttpStatus.NOT_FOUND);
+		CallSetEntity callSet = callSetService.getCallSetEntity(request.getCallSetDbId());
+		VariantEntity variant = variantService.getVariantEntity(request.getVariantDbId());
+		assertNoDuplicateCall(callSet.getId(), variant.getId(), callDbId);
+		if (request.getReadDepth() != null && request.getReadDepth() < 0) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "readDepth cannot be negative");
+		}
+		updateEntity(entity, request, callSet, variant);
+		Call saved = convertFromEntity(callRepository.save(entity));
+		if (variant.getVariantSet() != null) {
+			callSetService.ensureVariantSetBinding(callSet.getId(), variant.getVariantSet().getId());
+		}
+		return saved;
+	}
+
+	public Call deleteCall(String callDbId) throws BrAPIServerException {
+		CallEntity entity = getCallEntity(callDbId, HttpStatus.NOT_FOUND);
+		Call deleted = convertFromEntity(entity);
+		try {
+			callRepository.delete(entity);
+			callRepository.flush();
+		} catch (DataIntegrityViolationException e) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT, "Call cannot be deleted");
+		}
+		return deleted;
+	}
+
+	private void assertNoDuplicateCall(String callSetDbId, String variantDbId, String excludeCallDbId)
+			throws BrAPIServerException {
+		Pageable pageReq = PageRequest.of(0, 1);
+		SearchQueryBuilder<CallEntity> searchQuery = new SearchQueryBuilder<CallEntity>(CallEntity.class)
+				.appendSingle(callSetDbId, "callSet.id")
+				.appendSingle(variantDbId, "variant.id");
+		Page<CallEntity> page = callRepository.findAllBySearch(searchQuery, pageReq);
+		if (page.getTotalElements() > 0) {
+			CallEntity existing = page.getContent().get(0);
+			if (excludeCallDbId == null || !excludeCallDbId.equals(existing.getId())) {
+				throw new BrAPIServerException(HttpStatus.CONFLICT,
+						"Call already exists for this callSet and variant");
+			}
+		}
+	}
+
+	private void updateEntity(CallEntity entity, CallWriteRequest request, CallSetEntity callSet,
+			VariantEntity variant) {
+		entity.setCallSet(callSet);
+		entity.setVariant(variant);
+		entity.setGenotype(request.getGenotype().trim());
+		entity.setReadDepth(request.getReadDepth());
+		entity.setGenotypeLikelihood(request.getGenotypeLikelihood());
+		entity.setPhaseSet(request.getPhaseSet());
+	}
+
+	private void ensureVariantSetBindings(List<Call> calls) throws BrAPIServerException {
+		Set<String> processed = new HashSet<>();
+		for (Call call : calls) {
+			if (call.getCallSetDbId() == null || call.getVariantSetDbId() == null) {
+				continue;
+			}
+			String key = call.getCallSetDbId() + "|" + call.getVariantSetDbId();
+			if (processed.add(key)) {
+				callSetService.ensureVariantSetBinding(call.getCallSetDbId(), call.getVariantSetDbId());
+			}
+		}
+	}
 }

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

@@ -1,16 +1,25 @@
 package org.brapi.test.BrAPITestServer.service.geno;
 
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.LinkedHashSet;
 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.CallSetWriteRequest;
 import org.brapi.test.BrAPITestServer.model.entity.geno.CallSetEntity;
+import org.brapi.test.BrAPITestServer.model.entity.geno.SampleEntity;
+import org.brapi.test.BrAPITestServer.model.entity.geno.VariantSetEntity;
+import org.brapi.test.BrAPITestServer.repository.geno.CallRepository;
 import org.brapi.test.BrAPITestServer.repository.geno.CallSetRepository;
+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.Pageable;
 import org.springframework.http.HttpStatus;
@@ -24,9 +33,16 @@ import io.swagger.model.geno.CallSetsSearchRequest;
 public class CallSetService {
 
 	private final CallSetRepository callSetRepository;
+	private final CallRepository callRepository;
+	private final SampleService sampleService;
+	private final VariantSetRepository variantSetRepository;
 
-	public CallSetService(CallSetRepository callSetRepository) {
+	public CallSetService(CallSetRepository callSetRepository, CallRepository callRepository,
+			SampleService sampleService, VariantSetRepository variantSetRepository) {
 		this.callSetRepository = callSetRepository;
+		this.callRepository = callRepository;
+		this.sampleService = sampleService;
+		this.variantSetRepository = variantSetRepository;
 	}
 
 	public List<CallSet> findCallSets(String callSetDbId, String callSetName, String variantSetDbId, String sampleDbId,
@@ -111,4 +127,101 @@ public class CallSetService {
 	public CallSetEntity save(CallSetEntity entity) {
 		return callSetRepository.save(entity);
 	}
+
+	public void ensureVariantSetBinding(String callSetDbId, String variantSetDbId) throws BrAPIServerException {
+		if (callSetDbId == null || callSetDbId.isBlank() || variantSetDbId == null || variantSetDbId.isBlank()) {
+			return;
+		}
+		CallSetEntity callSet = getCallSetEntity(callSetDbId.trim());
+		VariantSetEntity variantSet = variantSetRepository.findById(variantSetDbId.trim())
+				.orElseThrow(() -> new BrAPIServerDbIdNotFoundException("variantSet", variantSetDbId,
+						HttpStatus.BAD_REQUEST));
+		if (callSet.getVariantSets() == null) {
+			callSet.setVariantSets(new ArrayList<>());
+		}
+		boolean exists = callSet.getVariantSets().stream().anyMatch(item -> variantSetDbId.trim().equals(item.getId()));
+		if (!exists) {
+			callSet.getVariantSets().add(variantSet);
+			callSet.setUpdated(new Date());
+			callSetRepository.save(callSet);
+		}
+	}
+
+	public CallSet saveCallSet(CallSetWriteRequest request) throws BrAPIServerException {
+		if (request.getCallSetName() == null || request.getCallSetName().isBlank()) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "callSetName is required");
+		}
+		if (request.getSampleDbId() == null || request.getSampleDbId().isBlank()) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "sampleDbId is required");
+		}
+		if (request.getCallSetDbId() != null && callSetRepository.findById(request.getCallSetDbId()).isPresent()) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT, "CallSet already exists: " + request.getCallSetDbId());
+		}
+		CallSetEntity entity = new CallSetEntity();
+		if (request.getCallSetDbId() != null && !request.getCallSetDbId().isBlank()) {
+			entity.setId(request.getCallSetDbId().trim());
+		}
+		entity.setCreated(new Date());
+		entity.setUpdated(new Date());
+		updateEntity(entity, request);
+		return convertFromEntity(callSetRepository.save(entity));
+	}
+
+	public CallSet updateCallSet(String callSetDbId, CallSetWriteRequest request) throws BrAPIServerException {
+		CallSetEntity entity = getCallSetEntity(callSetDbId, HttpStatus.NOT_FOUND);
+		entity.setUpdated(new Date());
+		updateEntity(entity, request);
+		return convertFromEntity(callSetRepository.save(entity));
+	}
+
+	public CallSet deleteCallSet(String callSetDbId) throws BrAPIServerException {
+		CallSetEntity entity = getCallSetEntity(callSetDbId, HttpStatus.NOT_FOUND);
+		assertNoCallSetDependencies(callSetDbId);
+		CallSet deleted = convertFromEntity(entity);
+		try {
+			callSetRepository.delete(entity);
+			callSetRepository.flush();
+		} catch (DataIntegrityViolationException e) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT, "CallSet is in use and cannot be deleted");
+		}
+		return deleted;
+	}
+
+	private void assertNoCallSetDependencies(String callSetDbId) throws BrAPIServerException {
+		if (callRepository.countByCallSetDbId(callSetDbId) > 0) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT, "CallSet is referenced by allele_call records");
+		}
+	}
+
+	private void updateEntity(CallSetEntity entity, CallSetWriteRequest request) throws BrAPIServerException {
+		if (request.getCallSetName() != null && !request.getCallSetName().isBlank()) {
+			entity.setCallSetName(request.getCallSetName().trim());
+		} else if (entity.getCallSetName() == null || entity.getCallSetName().isBlank()) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "callSetName is required");
+		}
+		if (request.getSampleDbId() != null && !request.getSampleDbId().isBlank()) {
+			SampleEntity sample = sampleService.getSampleEntity(request.getSampleDbId());
+			entity.setSample(sample);
+		} else if (entity.getSample() == null) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "sampleDbId is required");
+		}
+		if (request.getVariantSetDbIds() != null) {
+			List<VariantSetEntity> variantSets = new ArrayList<>();
+			LinkedHashSet<String> seen = new LinkedHashSet<>();
+			for (String variantSetDbId : request.getVariantSetDbIds()) {
+				if (variantSetDbId == null || variantSetDbId.isBlank()) {
+					continue;
+				}
+				String normalizedId = variantSetDbId.trim();
+				if (!seen.add(normalizedId)) {
+					continue;
+				}
+				VariantSetEntity variantSet = variantSetRepository.findById(normalizedId)
+						.orElseThrow(() -> new BrAPIServerDbIdNotFoundException("variantSet", variantSetDbId,
+								HttpStatus.BAD_REQUEST));
+				variantSets.add(variantSet);
+			}
+			entity.setVariantSets(variantSets);
+		}
+	}
 }

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

@@ -5,15 +5,22 @@ import java.util.Optional;
 
 import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerDbIdNotFoundException;
 import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerException;
+import org.brapi.test.BrAPITestServer.model.dto.geno.GenomeMapWriteRequest;
+import org.brapi.test.BrAPITestServer.model.dto.geno.LinkageGroupWriteRequest;
 import org.brapi.test.BrAPITestServer.model.entity.geno.GenomeMapEntity;
 import org.brapi.test.BrAPITestServer.model.entity.geno.LinkageGroupEntity;
+import org.brapi.test.BrAPITestServer.model.entity.geno.MarkerPositionEntity;
 import org.brapi.test.BrAPITestServer.repository.geno.GenomeMapRepository;
 import org.brapi.test.BrAPITestServer.repository.geno.LinkageGroupRepository;
+import org.brapi.test.BrAPITestServer.repository.geno.MarkerPositionRepository;
 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.core.CropService;
 import org.springframework.beans.factory.annotation.Autowired;
+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;
@@ -25,13 +32,18 @@ import io.swagger.model.geno.LinkageGroup;
 @Service
 public class GenomeMapService {
 
-	private GenomeMapRepository genomeMapRepository;
+	private final GenomeMapRepository genomeMapRepository;
-	private LinkageGroupRepository linkageGroupRepository;
+	private final LinkageGroupRepository linkageGroupRepository;
+	private final MarkerPositionRepository markerPositionRepository;
+	private final CropService cropService;
 
 	@Autowired
-	public GenomeMapService(GenomeMapRepository genomeMapRepository, LinkageGroupRepository linkageGroupRepository) {
+	public GenomeMapService(GenomeMapRepository genomeMapRepository, LinkageGroupRepository linkageGroupRepository,
+			MarkerPositionRepository markerPositionRepository, CropService cropService) {
 		this.genomeMapRepository = genomeMapRepository;
 		this.linkageGroupRepository = linkageGroupRepository;
+		this.markerPositionRepository = markerPositionRepository;
+		this.cropService = cropService;
 	}
 
 	public List<GenomeMap> findMaps(String commonCropName, String mapPUI, String scientificName, String type,
@@ -74,11 +86,183 @@ public class GenomeMapService {
 
 		Pageable pageReq = PagingUtility.getPageRequest(metadata);
 		Page<LinkageGroupEntity> page = linkageGroupRepository.findAllBySearch(searchQuery, pageReq);
-		List<LinkageGroup> linkageGroups = page.map(this::convertFromEntity).getContent();
+		List<LinkageGroup> linkageGroups = page.map(this::convertLinkageGroupFromEntity).getContent();
 		PagingUtility.calculateMetaData(metadata, page);
 		return linkageGroups;
 	}
 
+	public GenomeMap saveMap(GenomeMapWriteRequest request) throws BrAPIServerException {
+		if (request.getMapName() == null || request.getMapName().isBlank()) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "mapName is required");
+		}
+		if (request.getMapDbId() != null && genomeMapRepository.findById(request.getMapDbId()).isPresent()) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT, "GenomeMap already exists: " + request.getMapDbId());
+		}
+		GenomeMapEntity entity = new GenomeMapEntity();
+		if (request.getMapDbId() != null && !request.getMapDbId().isBlank()) {
+			entity.setId(request.getMapDbId().trim());
+		}
+		updateMapEntity(entity, request);
+		entity = genomeMapRepository.save(entity);
+		ensureMapPUI(entity);
+		return convertFromEntity(genomeMapRepository.save(entity));
+	}
+
+	public GenomeMap updateMap(String mapDbId, GenomeMapWriteRequest request) throws BrAPIServerException {
+		GenomeMapEntity entity = getMapEntity(mapDbId);
+		updateMapEntity(entity, request);
+		return convertFromEntity(genomeMapRepository.save(entity));
+	}
+
+	public GenomeMap deleteMap(String mapDbId) throws BrAPIServerException {
+		GenomeMapEntity entity = getMapEntity(mapDbId);
+		assertNoMapDependencies(mapDbId);
+		GenomeMap deleted = convertFromEntity(entity);
+		try {
+			genomeMapRepository.delete(entity);
+			genomeMapRepository.flush();
+		} catch (DataIntegrityViolationException e) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT, "GenomeMap is in use and cannot be deleted");
+		}
+		return deleted;
+	}
+
+	public LinkageGroup saveLinkageGroup(String mapDbId, LinkageGroupWriteRequest request) throws BrAPIServerException {
+		if (request.getLinkageGroupName() == null || request.getLinkageGroupName().isBlank()) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "linkageGroupName is required");
+		}
+		if (request.getLinkageGroupDbId() != null
+				&& linkageGroupRepository.findById(request.getLinkageGroupDbId()).isPresent()) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT,
+					"LinkageGroup already exists: " + request.getLinkageGroupDbId());
+		}
+		GenomeMapEntity map = getMapEntity(mapDbId);
+		assertLinkageGroupNameUnique(map.getId(), request.getLinkageGroupName().trim(), null);
+		LinkageGroupEntity entity = new LinkageGroupEntity();
+		if (request.getLinkageGroupDbId() != null && !request.getLinkageGroupDbId().isBlank()) {
+			entity.setId(request.getLinkageGroupDbId().trim());
+		}
+		entity.setGenomeMap(map);
+		updateLinkageGroupEntity(entity, request);
+		return convertLinkageGroupFromEntity(linkageGroupRepository.save(entity));
+	}
+
+	public LinkageGroup updateLinkageGroup(String mapDbId, String linkageGroupDbId, LinkageGroupWriteRequest request)
+			throws BrAPIServerException {
+		LinkageGroupEntity entity = getLinkageGroupEntity(linkageGroupDbId);
+		if (entity.getGenomeMap() == null || !mapDbId.equals(entity.getGenomeMap().getId())) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "LinkageGroup does not belong to map: " + mapDbId);
+		}
+		if (request.getLinkageGroupName() != null && !request.getLinkageGroupName().isBlank()) {
+			assertLinkageGroupNameUnique(mapDbId, request.getLinkageGroupName().trim(), linkageGroupDbId);
+		}
+		updateLinkageGroupEntity(entity, request);
+		return convertLinkageGroupFromEntity(linkageGroupRepository.save(entity));
+	}
+
+	public LinkageGroup deleteLinkageGroup(String mapDbId, String linkageGroupDbId) throws BrAPIServerException {
+		LinkageGroupEntity entity = getLinkageGroupEntity(linkageGroupDbId);
+		if (entity.getGenomeMap() == null || !mapDbId.equals(entity.getGenomeMap().getId())) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "LinkageGroup does not belong to map: " + mapDbId);
+		}
+		assertNoLinkageGroupDependencies(linkageGroupDbId);
+		LinkageGroup deleted = convertLinkageGroupFromEntity(entity);
+		try {
+			linkageGroupRepository.delete(entity);
+			linkageGroupRepository.flush();
+		} catch (DataIntegrityViolationException e) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT, "LinkageGroup is in use and cannot be deleted");
+		}
+		return deleted;
+	}
+
+	public GenomeMapEntity getMapEntity(String mapDbId) throws BrAPIServerException {
+		return genomeMapRepository.findById(mapDbId)
+				.orElseThrow(() -> new BrAPIServerDbIdNotFoundException("map", mapDbId, HttpStatus.NOT_FOUND));
+	}
+
+	public LinkageGroupEntity getLinkageGroupEntity(String linkageGroupDbId) throws BrAPIServerException {
+		return linkageGroupRepository.findById(linkageGroupDbId).orElseThrow(
+				() -> new BrAPIServerDbIdNotFoundException("linkageGroup", linkageGroupDbId, HttpStatus.NOT_FOUND));
+	}
+
+	private void assertNoMapDependencies(String mapDbId) throws BrAPIServerException {
+		Pageable pageReq = PageRequest.of(0, 1);
+		SearchQueryBuilder<LinkageGroupEntity> query = new SearchQueryBuilder<LinkageGroupEntity>(LinkageGroupEntity.class)
+				.appendSingle(mapDbId, "genomeMap.id");
+		if (linkageGroupRepository.findAllBySearch(query, pageReq).getTotalElements() > 0) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT, "GenomeMap is referenced by linkage group records");
+		}
+	}
+
+	private void assertNoLinkageGroupDependencies(String linkageGroupDbId) throws BrAPIServerException {
+		Pageable pageReq = PageRequest.of(0, 1);
+		SearchQueryBuilder<MarkerPositionEntity> query = new SearchQueryBuilder<MarkerPositionEntity>(
+				MarkerPositionEntity.class).appendSingle(linkageGroupDbId, "linkageGroup.id");
+		if (markerPositionRepository.findAllBySearch(query, pageReq).getTotalElements() > 0) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT,
+					"LinkageGroup is referenced by marker_position records");
+		}
+	}
+
+	private void assertLinkageGroupNameUnique(String mapDbId, String linkageGroupName, String excludeId)
+			throws BrAPIServerException {
+		SearchQueryBuilder<LinkageGroupEntity> query = new SearchQueryBuilder<LinkageGroupEntity>(LinkageGroupEntity.class)
+				.appendSingle(mapDbId, "genomeMap.id")
+				.appendSingle(linkageGroupName, "linkageGroupName");
+		Page<LinkageGroupEntity> page = linkageGroupRepository.findAllBySearch(query, PageRequest.of(0, 2));
+		for (LinkageGroupEntity existing : page.getContent()) {
+			if (excludeId == null || !excludeId.equals(existing.getId())) {
+				throw new BrAPIServerException(HttpStatus.CONFLICT,
+						"linkageGroupName already exists on this map: " + linkageGroupName);
+			}
+		}
+	}
+
+	private void ensureMapPUI(GenomeMapEntity entity) {
+		if (entity.getMapPUI() == null || entity.getMapPUI().isBlank()) {
+			entity.setMapPUI("urn:uuid:" + entity.getId());
+		}
+	}
+
+	private void updateMapEntity(GenomeMapEntity entity, GenomeMapWriteRequest request) throws BrAPIServerException {
+		entity.setMapName(request.getMapName().trim());
+		entity.setScientificName(trimOrNull(request.getScientificName()));
+		entity.setType(trimOrNull(request.getType()));
+		entity.setUnit(trimOrNull(request.getUnit()));
+		entity.setComments(trimOrNull(request.getComments()));
+		entity.setDocumentationURL(trimOrNull(request.getDocumentationURL()));
+		if (request.getPublishedDate() != null) {
+			entity.setPublishedDate(DateUtility.toDate(request.getPublishedDate()));
+		}
+		if (request.getCommonCropName() != null && !request.getCommonCropName().isBlank()) {
+			entity.setCrop(cropService.getCropEntity(request.getCommonCropName().trim()));
+		} else if (request.getCommonCropName() != null) {
+			entity.setCrop(null);
+		}
+	}
+
+	private void updateLinkageGroupEntity(LinkageGroupEntity entity, LinkageGroupWriteRequest request)
+			throws BrAPIServerException {
+		if (request.getLinkageGroupName() != null && !request.getLinkageGroupName().isBlank()) {
+			entity.setLinkageGroupName(request.getLinkageGroupName().trim());
+		}
+		if (request.getMaxPosition() != null) {
+			if (request.getMaxPosition() < 0) {
+				throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "maxPosition cannot be negative");
+			}
+			entity.setMaxMarkerPosition(request.getMaxPosition());
+		}
+	}
+
+	private String trimOrNull(String value) {
+		if (value == null) {
+			return null;
+		}
+		String trimmed = value.trim();
+		return trimmed.isEmpty() ? null : trimmed;
+	}
+
 	private GenomeMap convertFromEntity(GenomeMapEntity entity) {
 		GenomeMap map = new GenomeMap();
 		map.setAdditionalInfo(entity.getAdditionalInfoMap());
@@ -102,12 +286,18 @@ public class GenomeMapService {
 		return map;
 	}
 
-	private LinkageGroup convertFromEntity(LinkageGroupEntity entity) {
+	private LinkageGroup convertLinkageGroupFromEntity(LinkageGroupEntity entity) {
 		LinkageGroup group = new LinkageGroup();
 		group.setAdditionalInfo(entity.getAdditionalInfoMap());
 		group.setLinkageGroupName(entity.getLinkageGroupName());
-		group.setMarkerCount(entity.getMarkers().size());
+		int markerCount = entity.getMarkers() != null ? entity.getMarkers().size() : 0;
+		group.setMarkerCount(markerCount);
 		group.setMaxPosition(entity.getMaxMarkerPosition());
+		group.putAdditionalInfoItem("linkageGroupDbId", entity.getId());
+		if (entity.getGenomeMap() != null) {
+			group.putAdditionalInfoItem("mapDbId", entity.getGenomeMap().getId());
+			group.putAdditionalInfoItem("mapName", entity.getGenomeMap().getMapName());
+		}
 		return group;
 	}
 

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

@@ -2,12 +2,20 @@ package org.brapi.test.BrAPITestServer.service.geno;
 
 import java.util.List;
 
+import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerDbIdNotFoundException;
+import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerException;
+import org.brapi.test.BrAPITestServer.model.dto.geno.MarkerPositionWriteRequest;
+import org.brapi.test.BrAPITestServer.model.entity.geno.LinkageGroupEntity;
 import org.brapi.test.BrAPITestServer.model.entity.geno.MarkerPositionEntity;
+import org.brapi.test.BrAPITestServer.model.entity.geno.VariantEntity;
 import org.brapi.test.BrAPITestServer.repository.geno.MarkerPositionRepository;
 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;
 
 import io.swagger.model.Metadata;
@@ -18,9 +26,14 @@ import io.swagger.model.geno.MarkerPosition;
 public class MarkerPositionService {
 
 	private final MarkerPositionRepository markerPositionRepository;
+	private final GenomeMapService genomeMapService;
+	private final VariantService variantService;
 
-	public MarkerPositionService(MarkerPositionRepository markerPositionRepository) {
+	public MarkerPositionService(MarkerPositionRepository markerPositionRepository, GenomeMapService genomeMapService,
+			VariantService variantService) {
 		this.markerPositionRepository = markerPositionRepository;
+		this.genomeMapService = genomeMapService;
+		this.variantService = variantService;
 	}
 
 	public List<MarkerPosition> findMarkerPositions(String mapDbId, String linkageGroupName, String variantDbId,
@@ -52,11 +65,91 @@ public class MarkerPositionService {
 		return markerPositions;
 	}
 
+	public MarkerPosition saveMarkerPosition(MarkerPositionWriteRequest request) throws BrAPIServerException {
+		if (request.getLinkageGroupDbId() == null || request.getLinkageGroupDbId().isBlank()) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "linkageGroupDbId is required");
+		}
+		if (request.getVariantDbId() == null || request.getVariantDbId().isBlank()) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "variantDbId is required");
+		}
+		if (request.getPosition() == null) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "position is required");
+		}
+		if (request.getMarkerPositionDbId() != null
+				&& markerPositionRepository.findById(request.getMarkerPositionDbId()).isPresent()) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT,
+					"MarkerPosition already exists: " + request.getMarkerPositionDbId());
+		}
+		MarkerPositionEntity entity = new MarkerPositionEntity();
+		if (request.getMarkerPositionDbId() != null && !request.getMarkerPositionDbId().isBlank()) {
+			entity.setId(request.getMarkerPositionDbId().trim());
+		}
+		updateMarkerPositionEntity(entity, request);
+		return convertFromEntity(markerPositionRepository.save(entity));
+	}
+
+	public MarkerPosition updateMarkerPosition(String markerPositionDbId, MarkerPositionWriteRequest request)
+			throws BrAPIServerException {
+		MarkerPositionEntity entity = getMarkerPositionEntity(markerPositionDbId);
+		updateMarkerPositionEntity(entity, request);
+		return convertFromEntity(markerPositionRepository.save(entity));
+	}
+
+	public MarkerPosition deleteMarkerPosition(String markerPositionDbId) throws BrAPIServerException {
+		MarkerPositionEntity entity = getMarkerPositionEntity(markerPositionDbId);
+		MarkerPosition deleted = convertFromEntity(entity);
+		try {
+			markerPositionRepository.delete(entity);
+			markerPositionRepository.flush();
+		} catch (DataIntegrityViolationException e) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT, "MarkerPosition cannot be deleted");
+		}
+		return deleted;
+	}
+
+	public MarkerPositionEntity getMarkerPositionEntity(String markerPositionDbId) throws BrAPIServerException {
+		return markerPositionRepository.findById(markerPositionDbId).orElseThrow(
+				() -> new BrAPIServerDbIdNotFoundException("markerPosition", markerPositionDbId, HttpStatus.NOT_FOUND));
+	}
+
+	private void updateMarkerPositionEntity(MarkerPositionEntity entity, MarkerPositionWriteRequest request)
+			throws BrAPIServerException {
+		LinkageGroupEntity linkageGroup = genomeMapService.getLinkageGroupEntity(request.getLinkageGroupDbId());
+		VariantEntity variant = variantService.getVariantEntity(request.getVariantDbId());
+		assertMarkerVariantUnique(linkageGroup.getId(), variant.getId(), entity.getId());
+		if (request.getPosition() < 0) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "position cannot be negative");
+		}
+		if (linkageGroup.getMaxMarkerPosition() != null
+				&& request.getPosition() > linkageGroup.getMaxMarkerPosition()) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST,
+					"position cannot exceed linkage group maxPosition");
+		}
+		entity.setLinkageGroup(linkageGroup);
+		entity.setVariant(variant);
+		entity.setPosition(request.getPosition());
+	}
+
+	private void assertMarkerVariantUnique(String linkageGroupDbId, String variantDbId, String excludeId)
+			throws BrAPIServerException {
+		SearchQueryBuilder<MarkerPositionEntity> query = new SearchQueryBuilder<MarkerPositionEntity>(
+				MarkerPositionEntity.class).appendSingle(linkageGroupDbId, "linkageGroup.id")
+						.appendSingle(variantDbId, "variant.id");
+		Page<MarkerPositionEntity> page = markerPositionRepository.findAllBySearch(query, PageRequest.of(0, 2));
+		for (MarkerPositionEntity existing : page.getContent()) {
+			if (excludeId == null || !excludeId.equals(existing.getId())) {
+				throw new BrAPIServerException(HttpStatus.CONFLICT,
+						"variant already has a marker position on this linkage group");
+			}
+		}
+	}
+
 	private MarkerPosition convertFromEntity(MarkerPositionEntity entity) {
 		MarkerPosition position = new MarkerPosition();
 		position.setAdditionalInfo(entity.getAdditionalInfoMap());
 		if (entity.getLinkageGroup() != null) {
 			position.setLinkageGroupName(entity.getLinkageGroup().getLinkageGroupName());
+			position.putAdditionalInfoItem("linkageGroupDbId", entity.getLinkageGroup().getId());
 			if (entity.getLinkageGroup().getGenomeMap() != null) {
 				position.setMapDbId(entity.getLinkageGroup().getGenomeMap().getId());
 				position.setMapName(entity.getLinkageGroup().getGenomeMap().getMapName());
@@ -67,6 +160,7 @@ public class MarkerPositionService {
 			position.setVariantDbId(entity.getVariant().getId());
 			position.setVariantName(entity.getVariant().getVariantName());
 		}
+		position.putAdditionalInfoItem("markerPositionDbId", entity.getId());
 		return position;
 	}
 

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

@@ -0,0 +1,134 @@
+package org.brapi.test.BrAPITestServer.service.geno;
+
+import java.util.ArrayList;
+import java.util.List;
+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.VariantSetAnalysisWriteRequest;
+import org.brapi.test.BrAPITestServer.model.entity.geno.VariantSetAnalysisEntity;
+import org.brapi.test.BrAPITestServer.model.entity.geno.VariantSetEntity;
+import org.brapi.test.BrAPITestServer.repository.geno.VariantSetAnalysisRepository;
+import org.brapi.test.BrAPITestServer.service.DateUtility;
+import org.springframework.dao.DataIntegrityViolationException;
+import org.springframework.http.HttpStatus;
+import org.springframework.stereotype.Service;
+
+import io.swagger.model.geno.Analysis;
+
+@Service
+public class VariantSetAnalysisService {
+
+	private final VariantSetAnalysisRepository variantSetAnalysisRepository;
+	private final VariantSetService variantSetService;
+
+	public VariantSetAnalysisService(VariantSetAnalysisRepository variantSetAnalysisRepository,
+			VariantSetService variantSetService) {
+		this.variantSetAnalysisRepository = variantSetAnalysisRepository;
+		this.variantSetService = variantSetService;
+	}
+
+	public List<Analysis> findAnalysisByVariantSet(String variantSetDbId) throws BrAPIServerException {
+		assertVariantSetExists(variantSetDbId);
+		return variantSetAnalysisRepository.findByVariantSet_Id(variantSetDbId).stream()
+				.map(this::convertFromEntity)
+				.collect(Collectors.toList());
+	}
+
+	public Analysis saveAnalysis(String variantSetDbId, VariantSetAnalysisWriteRequest request)
+			throws BrAPIServerException {
+		VariantSetEntity variantSet = variantSetService.getVariantSetEntity(variantSetDbId);
+		if (request.getAnalysisName() == null || request.getAnalysisName().isBlank()) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "analysisName is required");
+		}
+		if (request.getAnalysisDbId() != null
+				&& variantSetAnalysisRepository.findById(request.getAnalysisDbId()).isPresent()) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT,
+					"Analysis already exists: " + request.getAnalysisDbId());
+		}
+		VariantSetAnalysisEntity entity = new VariantSetAnalysisEntity();
+		if (request.getAnalysisDbId() != null && !request.getAnalysisDbId().isBlank()) {
+			entity.setId(request.getAnalysisDbId().trim());
+		}
+		updateEntity(entity, variantSet, request);
+		return convertFromEntity(variantSetAnalysisRepository.save(entity));
+	}
+
+	public Analysis updateAnalysis(String variantSetDbId, String analysisDbId, VariantSetAnalysisWriteRequest request)
+			throws BrAPIServerException {
+		VariantSetAnalysisEntity entity = getAnalysisEntity(variantSetDbId, analysisDbId);
+		if (request.getAnalysisName() == null || request.getAnalysisName().isBlank()) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "analysisName is required");
+		}
+		updateEntity(entity, entity.getVariantSet(), request);
+		return convertFromEntity(variantSetAnalysisRepository.save(entity));
+	}
+
+	public Analysis deleteAnalysis(String variantSetDbId, String analysisDbId) throws BrAPIServerException {
+		VariantSetAnalysisEntity entity = getAnalysisEntity(variantSetDbId, analysisDbId);
+		Analysis deleted = convertFromEntity(entity);
+		try {
+			variantSetAnalysisRepository.delete(entity);
+			variantSetAnalysisRepository.flush();
+		} catch (DataIntegrityViolationException e) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT, "Analysis cannot be deleted");
+		}
+		return deleted;
+	}
+
+	private void assertVariantSetExists(String variantSetDbId) throws BrAPIServerException {
+		variantSetService.getVariantSetEntity(variantSetDbId);
+	}
+
+	private VariantSetAnalysisEntity getAnalysisEntity(String variantSetDbId, String analysisDbId)
+			throws BrAPIServerException {
+		VariantSetAnalysisEntity entity = variantSetAnalysisRepository.findById(analysisDbId).orElseThrow(
+				() -> new BrAPIServerDbIdNotFoundException("analysis", analysisDbId, HttpStatus.NOT_FOUND));
+		if (entity.getVariantSet() == null || !variantSetDbId.equals(entity.getVariantSet().getId())) {
+			throw new BrAPIServerDbIdNotFoundException("analysis", analysisDbId, HttpStatus.NOT_FOUND);
+		}
+		return entity;
+	}
+
+	private void updateEntity(VariantSetAnalysisEntity entity, VariantSetEntity variantSet,
+			VariantSetAnalysisWriteRequest request) throws BrAPIServerException {
+		entity.setVariantSet(variantSet);
+		entity.setAnalysisName(request.getAnalysisName().trim());
+		entity.setDescription(trimToNull(request.getDescription()));
+		entity.setType(trimToNull(request.getType()));
+		entity.setCreated(DateUtility.toDate(request.getCreated()));
+		entity.setUpdated(DateUtility.toDate(request.getUpdated()));
+		entity.setSoftware(normalizeSoftware(request.getSoftware()));
+	}
+
+	private List<String> normalizeSoftware(List<String> software) {
+		if (software == null) {
+			return new ArrayList<>();
+		}
+		return software.stream()
+				.map(this::trimToNull)
+				.filter(item -> item != null && !item.isBlank())
+				.collect(Collectors.toList());
+	}
+
+	private String trimToNull(String value) {
+		if (value == null) {
+			return null;
+		}
+		String trimmed = value.trim();
+		return trimmed.isEmpty() ? null : trimmed;
+	}
+
+	private Analysis convertFromEntity(VariantSetAnalysisEntity entity) {
+		Analysis analysis = new Analysis();
+		analysis.setAnalysisDbId(entity.getId());
+		analysis.setAnalysisName(entity.getAnalysisName());
+		analysis.setCreated(DateUtility.toOffsetDateTime(entity.getCreated()));
+		analysis.setDescription(entity.getDescription());
+		analysis.setSoftware(entity.getSoftware());
+		analysis.setType(entity.getType());
+		analysis.setUpdated(DateUtility.toOffsetDateTime(entity.getUpdated()));
+		return analysis;
+	}
+}

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

@@ -0,0 +1,148 @@
+package org.brapi.test.BrAPITestServer.service.geno;
+
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.List;
+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.VariantSetAvailableFormatRecord;
+import org.brapi.test.BrAPITestServer.model.dto.geno.VariantSetAvailableFormatWriteRequest;
+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.VariantSetAvailableFormatRepository;
+import org.springframework.dao.DataIntegrityViolationException;
+import org.springframework.http.HttpStatus;
+import org.springframework.stereotype.Service;
+
+import io.swagger.model.geno.GenoFileDataFormatEnum;
+
+@Service
+public class VariantSetAvailableFormatService {
+
+	private final VariantSetAvailableFormatRepository variantSetAvailableFormatRepository;
+	private final VariantSetService variantSetService;
+
+	public VariantSetAvailableFormatService(
+			VariantSetAvailableFormatRepository variantSetAvailableFormatRepository,
+			VariantSetService variantSetService) {
+		this.variantSetAvailableFormatRepository = variantSetAvailableFormatRepository;
+		this.variantSetService = variantSetService;
+	}
+
+	public List<VariantSetAvailableFormatRecord> findFormatsByVariantSet(String variantSetDbId)
+			throws BrAPIServerException {
+		variantSetService.getVariantSetEntity(variantSetDbId);
+		return variantSetAvailableFormatRepository.findByVariantSet_Id(variantSetDbId).stream()
+				.map(this::convertFromEntity)
+				.collect(Collectors.toList());
+	}
+
+	public VariantSetAvailableFormatRecord saveFormat(String variantSetDbId,
+			VariantSetAvailableFormatWriteRequest request) throws BrAPIServerException {
+		VariantSetEntity variantSet = variantSetService.getVariantSetEntity(variantSetDbId);
+		validateFormatRequest(request);
+		if (request.getFormatDbId() != null
+				&& variantSetAvailableFormatRepository.findById(request.getFormatDbId()).isPresent()) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT,
+					"Available format already exists: " + request.getFormatDbId());
+		}
+		VariantSetAvailableFormatEntity entity = new VariantSetAvailableFormatEntity();
+		if (request.getFormatDbId() != null && !request.getFormatDbId().isBlank()) {
+			entity.setId(request.getFormatDbId().trim());
+		}
+		updateEntity(entity, variantSet, request);
+		return convertFromEntity(variantSetAvailableFormatRepository.save(entity));
+	}
+
+	public VariantSetAvailableFormatRecord updateFormat(String variantSetDbId, String formatDbId,
+			VariantSetAvailableFormatWriteRequest request) throws BrAPIServerException {
+		VariantSetAvailableFormatEntity entity = getFormatEntity(variantSetDbId, formatDbId);
+		validateFormatRequest(request);
+		updateEntity(entity, entity.getVariantSet(), request);
+		return convertFromEntity(variantSetAvailableFormatRepository.save(entity));
+	}
+
+	public VariantSetAvailableFormatRecord deleteFormat(String variantSetDbId, String formatDbId)
+			throws BrAPIServerException {
+		VariantSetAvailableFormatEntity entity = getFormatEntity(variantSetDbId, formatDbId);
+		VariantSetAvailableFormatRecord deleted = convertFromEntity(entity);
+		try {
+			variantSetAvailableFormatRepository.delete(entity);
+			variantSetAvailableFormatRepository.flush();
+		} catch (DataIntegrityViolationException e) {
+			throw new BrAPIServerException(HttpStatus.CONFLICT, "Available format cannot be deleted");
+		}
+		return deleted;
+	}
+
+	private VariantSetAvailableFormatEntity getFormatEntity(String variantSetDbId, String formatDbId)
+			throws BrAPIServerException {
+		VariantSetAvailableFormatEntity entity = variantSetAvailableFormatRepository.findById(formatDbId).orElseThrow(
+				() -> new BrAPIServerDbIdNotFoundException("availableFormat", formatDbId, HttpStatus.NOT_FOUND));
+		if (entity.getVariantSet() == null || !variantSetDbId.equals(entity.getVariantSet().getId())) {
+			throw new BrAPIServerDbIdNotFoundException("availableFormat", formatDbId, HttpStatus.NOT_FOUND);
+		}
+		return entity;
+	}
+
+	private void validateFormatRequest(VariantSetAvailableFormatWriteRequest request) throws BrAPIServerException {
+		if (request.getDataFormat() == null || request.getDataFormat().isBlank()) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "dataFormat is required");
+		}
+		if (request.getFileFormat() == null || request.getFileFormat().isBlank()) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "fileFormat is required");
+		}
+		if (GenoFileDataFormatEnum.fromValue(request.getDataFormat()) == null) {
+			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "Invalid dataFormat: " + request.getDataFormat());
+		}
+		if (request.getFileURL() != null && !request.getFileURL().isBlank()) {
+			try {
+				new URL(request.getFileURL().trim());
+			} catch (MalformedURLException e) {
+				throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "Invalid fileURL: " + request.getFileURL());
+			}
+		}
+	}
+
+	private void updateEntity(VariantSetAvailableFormatEntity entity, VariantSetEntity variantSet,
+			VariantSetAvailableFormatWriteRequest request) {
+		entity.setVariantSet(variantSet);
+		entity.setDataFormat(GenoFileDataFormatEnum.fromValue(request.getDataFormat()));
+		entity.setFileFormat(io.swagger.model.WSMIMEDataTypes.fromValue(request.getFileFormat()));
+		entity.setFileURL(trimToNull(request.getFileURL()));
+		entity.setExpandHomozygotes(request.getExpandHomozygotes());
+		entity.setSepPhased(trimToNull(request.getSepPhased()));
+		entity.setSepUnphased(trimToNull(request.getSepUnphased()));
+		entity.setUnknownString(trimToNull(request.getUnknownString()));
+	}
+
+	private String trimToNull(String value) {
+		if (value == null) {
+			return null;
+		}
+		String trimmed = value.trim();
+		return trimmed.isEmpty() ? null : trimmed;
+	}
+
+	private VariantSetAvailableFormatRecord convertFromEntity(VariantSetAvailableFormatEntity entity) {
+		VariantSetAvailableFormatRecord record = new VariantSetAvailableFormatRecord();
+		record.setFormatDbId(entity.getId());
+		if (entity.getVariantSet() != null) {
+			record.setVariantSetDbId(entity.getVariantSet().getId());
+		}
+		if (entity.getDataFormat() != null) {
+			record.setDataFormat(entity.getDataFormat().toString());
+		}
+		if (entity.getFileFormat() != null) {
+			record.setFileFormat(entity.getFileFormat().toString());
+		}
+		record.setFileURL(entity.getFileURL());
+		record.setExpandHomozygotes(entity.getExpandHomozygotes());
+		record.setSepPhased(entity.getSepPhased());
+		record.setSepUnphased(entity.getSepUnphased());
+		record.setUnknownString(entity.getUnknownString());
+		return record;
+	}
+}