fix:java项目性能优化

2026-05-28 15:51:39 +08:00
parent 8b65de36b8
commit 3bdd16cbd2
54 changed files with 3178 additions and 624 deletions
--- a/frontend/src/app/(app)/genotyping/reference-set/api.ts
+++ b/frontend/src/app/(app)/genotyping/reference-set/api.ts
@@ -3,7 +3,10 @@ import { getAuthToken } from "@/utils/token";
 import {
  NONE_SELECT_VALUE,
  type ReferenceBasesRecord,
+  type ReferenceQuery,
  type ReferenceRecord,
+  type ReferenceSetPageOptions,
+  type ReferenceSetQuery,
  type ReferenceSetRecord,
  type SelectOption,
 } from "./types";
@@ -41,6 +44,11 @@ interface VariantSetResponse {
  referenceSetDbId: string | null;
 }

+interface VariantResponse {
+  variantDbId: string;
+  referenceSetDbId: string | null;
+}
+
 type ReferenceSetPayload = Partial<Record<
  | "id"
  | "reference_set_name"
@@ -86,7 +94,7 @@ async function request<T>(path: string, init?: RequestInit): Promise<T> {

  if (!response.ok) {
    const detail = await response.text();
-    throw new Error(detail || `Request failed: ${response.status}`);
+    throw new Error(detail || `请求失败：${response.status}`);
  }
  return response.json() as Promise<T>;
 }
@@ -105,7 +113,7 @@ const requiredText = (value: unknown, message: string) => {

 const optionalNumber = (value: unknown) => {
  const normalized = optionalText(value);
-  if (!normalized) return null;
+  if (normalized === null) return null;
  const parsed = Number(normalized);
  return Number.isNaN(parsed) ? null : parsed;
 };
@@ -125,19 +133,22 @@ const optionalUrl = (value: unknown, label: string) => {
  return normalized;
 };

-const validateBases = (value: unknown) => {
+const validateBases = (value: unknown, required = false) => {
  const normalized = optionalText(value);
-  if (!normalized) return null;
+  if (!normalized) {
+    if (required) throw new Error("碱基序列片段不能为空");
+    return null;
+  }
  if (normalized.length > 2048) {
    throw new Error("碱基序列片段不能超过 2048 字符");
  }
  if (!BASES_PATTERN.test(normalized)) {
-    throw new Error("碱基序列仅允许 A/C/G/T/N 及常见占位符");
+    throw new Error("碱基序列仅允<EFBFBD>?A/C/G/T/N 及常见占位符");
  }
  return normalized.toUpperCase();
 };

-const mapReferenceSet = (item: ReferenceSetRecord): ReferenceSetRecord => ({
+export const mapReferenceSet = (item: ReferenceSetRecord): ReferenceSetRecord => ({
  ...item,
  id: item.referenceSetDbId || item.id,
  reference_set_name: item.reference_set_name || item.referenceSetName || null,
@@ -166,7 +177,7 @@ const mapReferenceSet = (item: ReferenceSetRecord): ReferenceSetRecord => ({
    || null,
 });

-const mapReference = (reference: ReferenceRecord): ReferenceRecord => ({
+export const mapReference = (reference: ReferenceRecord): ReferenceRecord => ({
  ...reference,
  id: reference.referenceDbId || reference.id,
  reference_name: reference.reference_name || reference.referenceName || null,
@@ -175,7 +186,7 @@ const mapReference = (reference: ReferenceRecord): ReferenceRecord => ({
  source_divergence: reference.source_divergence ?? reference.sourceDivergence ?? null,
 });

-const mapReferenceBases = (item: ReferenceBasesRecord): ReferenceBasesRecord => ({
+export const mapReferenceBases = (item: ReferenceBasesRecord): ReferenceBasesRecord => ({
  ...item,
  id: item.referenceBasesDbId || item.id,
  reference_id: item.reference_id || item.referenceDbId || null,
@@ -183,63 +194,155 @@ const mapReferenceBases = (item: ReferenceBasesRecord): ReferenceBasesRecord =>
  page_number: item.page_number ?? item.pageNumber ?? null,
 });

-const referenceSetBody = (payload: ReferenceSetPayload) => ({
-  referenceSetName: requiredText(payload.reference_set_name, "ReferenceSet 名称不能为空"),
-  assemblyPUI: optionalText(payload.assembly_pui),
-  description: optionalText(payload.description),
-  isDerived: optionalBoolean(payload.is_derived),
-  md5checksum: optionalText(payload.md5checksum),
-  sourceURI: optionalUrl(payload.source_uri, "来源 URI"),
-  species: optionalText(payload.species_ontology_term) || optionalUrl(payload.species_ontology_termuri, "物种本体 URI")
-    ? {
-        term: optionalText(payload.species_ontology_term),
-        termURI: optionalUrl(payload.species_ontology_termuri, "物种本体 URI"),
-      }
-    : undefined,
-  sourceGermplasmDbId: optionalText(payload.source_germplasm_id),
-});
+function buildSpecies(payload: ReferenceSetPayload) {
+  const term = optionalText(payload.species_ontology_term);
+  const termURI = optionalUrl(payload.species_ontology_termuri, "物种本体 URI");
+  if (!term && !termURI) return undefined;
+  return { term, termURI };
+}

-const referenceBody = (payload: ReferencePayload) => ({
-  referenceName: requiredText(payload.reference_name, "Reference 名称不能为空"),
-  referenceSetDbId: requiredText(payload.reference_set_id, "ReferenceSet 不能为空"),
-  length: optionalNumber(payload.length),
-  md5checksum: optionalText(payload.md5checksum),
-  sourceDivergence: optionalNumber(payload.source_divergence),
-});
+function buildReferenceSetWriteBody(payload: ReferenceSetPayload) {
+  const body: Record<string, unknown> = {
+    referenceSetName: requiredText(payload.reference_set_name, "请填<EFBFBD>?ReferenceSet 名称"),
+  };
+  const optionalFields: Array<[string, unknown]> = [
+    ["assemblyPUI", optionalText(payload.assembly_pui)],
+    ["description", optionalText(payload.description)],
+    ["isDerived", optionalBoolean(payload.is_derived)],
+    ["md5checksum", optionalText(payload.md5checksum)],
+    ["sourceURI", optionalUrl(payload.source_uri, "来源 URI")],
+    ["sourceGermplasmDbId", optionalText(payload.source_germplasm_id)],
+  ];
+  optionalFields.forEach(([key, value]) => {
+    if (value !== null && value !== undefined) body[key] = value;
+  });
+  const species = buildSpecies(payload);
+  if (species) body.species = species;
+  return body;
+}

-const referenceBasesBody = (payload: ReferenceBasesPayload) => ({
-  referenceDbId: requiredText(payload.reference_id, "Reference 不能为空"),
-  pageNumber: optionalNumber(payload.page_number),
-  bases: validateBases(payload.bases),
-});
+function buildReferenceWriteBody(payload: ReferencePayload) {
+  const body: Record<string, unknown> = {
+    referenceName: requiredText(payload.reference_name, "请填<E8AFB7>?Reference 名称"),
+    referenceSetDbId: requiredText(payload.reference_set_id, "请选择 ReferenceSet"),
+  };
+  const length = optionalNumber(payload.length);
+  const sourceDivergence = optionalNumber(payload.source_divergence);
+  const md5checksum = optionalText(payload.md5checksum);
+  if (length !== null) {
+    if (length < 0) throw new Error("序列长度不能为负");
+    body.length = length;
+  }
+  if (sourceDivergence !== null) body.sourceDivergence = sourceDivergence;
+  if (md5checksum) body.md5checksum = md5checksum;
+  return body;
+}

-const attachReferenceSetCounts = (
+function buildReferenceBasesWriteBody(payload: ReferenceBasesPayload, creating: boolean) {
+  const pageNumber = optionalNumber(payload.page_number);
+  if (pageNumber === null) throw new Error("请填写分页序");
+  if (pageNumber < 0) throw new Error("分页序号不能为负");
+  return {
+    referenceDbId: requiredText(payload.reference_id, "请选择 Reference"),
+    pageNumber,
+    bases: validateBases(payload.bases, creating),
+  };
+}
+
+function filterReferenceSets(rows: ReferenceSetRecord[], query?: ReferenceSetQuery) {
+  const name = optionalText(query?.reference_set_name)?.toLowerCase();
+  const assembly = optionalText(query?.assembly_pui)?.toLowerCase();
+  return rows.filter((row) => {
+    if (name && !String(row.reference_set_name ?? "").toLowerCase().includes(name)) return false;
+    if (assembly && !String(row.assembly_pui ?? "").toLowerCase().includes(assembly)) return false;
+    return true;
+  });
+}
+
+function filterReferences(rows: ReferenceRecord[], query?: ReferenceQuery) {
+  const name = optionalText(query?.reference_name)?.toLowerCase();
+  const referenceSetId = optionalText(query?.reference_set_id);
+  return rows.filter((row) => {
+    if (referenceSetId && row.reference_set_id !== referenceSetId) return false;
+    if (name && !String(row.reference_name ?? "").toLowerCase().includes(name)) return false;
+    return true;
+  });
+}
+
+function attachReferenceSetCounts(
  rows: ReferenceSetRecord[],
  references: ReferenceRecord[],
  variantSets: VariantSetResponse[],
-) => rows.map((row) => ({
-  ...row,
-  reference_count: references.filter((item) => item.reference_set_id === row.id).length,
-  variantset_count: variantSets.filter((item) => item.referenceSetDbId === row.id).length,
-}));
+  variants: VariantResponse[],
+) {
+  return rows.map((row) => ({
+    ...row,
+    reference_count: references.filter((item) => item.reference_set_id === row.id).length,
+    variantset_count: variantSets.filter((item) => item.referenceSetDbId === row.id).length,
+    variant_count: variants.filter((item) => item.referenceSetDbId === row.id).length,
+  }));
+}
+
+function attachReferenceBasesStats(references: ReferenceRecord[], basesPages: ReferenceBasesRecord[]) {
+  return references.map((reference) => {
+    const pages = basesPages.filter((page) => page.reference_id === reference.id);
+    const basesTotalLength = pages.reduce((total, page) => total + String(page.bases ?? "").length, 0);
+    return {
+      ...reference,
+      bases_page_count: pages.length,
+      bases_total_length: basesTotalLength,
+    };
+  });
+}
+
+function enrichReferenceSetNames(
+  references: ReferenceRecord[],
+  referenceSets: ReferenceSetRecord[],
+): ReferenceRecord[] {
+  const label = new Map(referenceSets.map((item) => [item.id, item.reference_set_name || item.id]));
+  return references.map((reference) => ({
+    ...reference,
+    reference_set_name: reference.reference_set_id
+      ? label.get(reference.reference_set_id) ?? reference.reference_set_name
+      : reference.reference_set_name,
+  }));
+}
+
+function enrichGermplasmNames(
+  rows: ReferenceSetRecord[],
+  germplasm: SelectOption[],
+): ReferenceSetRecord[] {
+  const label = new Map(germplasm.map((item) => [item.value, item.label]));
+  return rows.map((row) => ({
+    ...row,
+    source_germplasm_name: row.source_germplasm_id
+      ? label.get(row.source_germplasm_id) ?? row.source_germplasm_name ?? row.source_germplasm_id
+      : row.source_germplasm_name,
+  }));
+}

 const referenceSetRowsLoader = createCachedLoader(async () => {
-  const response = await request<BrapiListResponse<ReferenceSetRecord>>("/brapi/v2/referencesets?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<ReferenceSetRecord>>("/brapi/v2/referencesets?page=0&pageSize=10");
  return response.result.data.map(mapReferenceSet);
 });

 const referenceRowsLoader = createCachedLoader(async () => {
-  const response = await request<BrapiListResponse<ReferenceRecord>>("/brapi/v2/references?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<ReferenceRecord>>("/brapi/v2/references?page=0&pageSize=10");
  return response.result.data.map(mapReference);
 });

 const variantSetRowsLoader = createCachedLoader(async () => {
-  const response = await request<BrapiListResponse<VariantSetResponse>>("/brapi/v2/variantsets?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<VariantSetResponse>>("/brapi/v2/variantsets?page=0&pageSize=10");
+  return response.result.data;
+});
+
+const variantRowsLoader = createCachedLoader(async () => {
+  const response = await request<BrapiListResponse<VariantResponse>>("/brapi/v2/variants?page=0&pageSize=10");
  return response.result.data;
 });

 const referenceBasesRowsLoader = createCachedLoader(async () => {
-  const response = await request<BrapiListResponse<ReferenceBasesRecord>>("/brapi/v2/referencebases?page=0&pageSize=1000");
+  const response = await request<BrapiListResponse<ReferenceBasesRecord>>("/brapi/v2/referencebases?page=0&pageSize=10");
  return response.result.data.map(mapReferenceBases);
 });

@@ -247,32 +350,11 @@ export function invalidateReferenceSetPageCache() {
  referenceSetRowsLoader.invalidate();
  referenceRowsLoader.invalidate();
  variantSetRowsLoader.invalidate();
+  variantRowsLoader.invalidate();
  referenceBasesRowsLoader.invalidate();
 }

-export async function fetchReferenceSetRows(force = false): Promise<ReferenceSetRecord[]> {
-  const [referenceSets, references, variantSets] = await Promise.all([
-    referenceSetRowsLoader.load(force),
-    referenceRowsLoader.load(force),
-    variantSetRowsLoader.load(force),
-  ]);
-
-  return attachReferenceSetCounts(referenceSets, references, variantSets);
-}
-
-export async function fetchReferenceRows(force = false): Promise<ReferenceRecord[]> {
-  return referenceRowsLoader.load(force);
-}
-
-export async function fetchReferenceBasesRows(force = false): Promise<ReferenceBasesRecord[]> {
-  return referenceBasesRowsLoader.load(force);
-}
-
-export async function fetchReferenceSetOptions(force = false): Promise<{
-  referenceSets: SelectOption[];
-  references: SelectOption[];
-  germplasm: SelectOption[];
-}> {
+export async function fetchReferenceSetOptions(force = false): Promise<ReferenceSetPageOptions> {
  const [sharedOptions, referenceSets, references] = await Promise.all([
    loadDropdownBundle({ germplasms: true }, force),
    referenceSetRowsLoader.load(force),
@@ -292,13 +374,127 @@ export async function fetchReferenceSetOptions(force = false): Promise<{
  };
 }

+export async function loadReferenceSetPageData(params: {
+  referenceSetQuery?: ReferenceSetQuery;
+  referenceQuery?: ReferenceQuery;
+  force?: boolean;
+} = {}) {
+  const force = params.force ?? false;
+  const [options, referenceSets, references, variantSets, variants, basesPages] = await Promise.all([
+    fetchReferenceSetOptions(force),
+    referenceSetRowsLoader.load(force),
+    referenceRowsLoader.load(force),
+    variantSetRowsLoader.load(force),
+    variantRowsLoader.load(force),
+    referenceBasesRowsLoader.load(force),
+  ]);
+
+  const enrichedSets = enrichGermplasmNames(
+    attachReferenceSetCounts(referenceSets, references, variantSets, variants),
+    options.germplasm,
+  );
+  const enrichedReferences = attachReferenceBasesStats(
+    enrichReferenceSetNames(references, referenceSets),
+    basesPages,
+  );
+
+  return {
+    options,
+    referenceSets: filterReferenceSets(enrichedSets, params.referenceSetQuery),
+    references: filterReferences(enrichedReferences, params.referenceQuery),
+    basesPages,
+    variantSets,
+    variants,
+  };
+}
+
+export async function fetchReferenceSetRows(query?: ReferenceSetQuery, force = false): Promise<ReferenceSetRecord[]> {
+  const { referenceSets } = await loadReferenceSetPageData({ referenceSetQuery: query, force });
+  return referenceSets;
+}
+
+export async function fetchReferenceRows(query?: ReferenceQuery, force = false): Promise<ReferenceRecord[]> {
+  const { references } = await loadReferenceSetPageData({ referenceQuery: query, force });
+  return references;
+}
+
+export async function fetchReferenceSetDetail(id: string): Promise<ReferenceSetRecord> {
+  const response = await request<BrapiSingleResponse<ReferenceSetRecord>>(
+    `/brapi/v2/referencesets/${encodeURIComponent(id)}`,
+  );
+  const { options, references, variantSets, variants } = await loadReferenceSetPageData();
+  const [detail] = enrichGermplasmNames(
+    attachReferenceSetCounts([mapReferenceSet(response.result)], references, variantSets, variants),
+    options.germplasm,
+  );
+  return detail;
+}
+
+export async function fetchReferenceDetail(id: string): Promise<ReferenceRecord> {
+  const response = await request<BrapiSingleResponse<ReferenceRecord>>(
+    `/brapi/v2/references/${encodeURIComponent(id)}`,
+  );
+  const { referenceSets, basesPages } = await loadReferenceSetPageData();
+  const [detail] = attachReferenceBasesStats(
+    enrichReferenceSetNames([mapReference(response.result)], referenceSets),
+    basesPages,
+  );
+  return detail;
+}
+
+export async function fetchReferenceBasesRows(referenceDbId?: string, force = false): Promise<ReferenceBasesRecord[]> {
+  const pages = await referenceBasesRowsLoader.load(force);
+  const filtered = referenceDbId
+    ? pages.filter((page) => page.reference_id === referenceDbId)
+    : pages;
+  return filtered.sort((a, b) => Number(a.page_number ?? 0) - Number(b.page_number ?? 0));
+}
+
+export function normalizeReferenceSetFormData(record: ReferenceSetRecord): Record<string, unknown> {
+  return {
+    id: record.id,
+    reference_set_name: record.reference_set_name ?? "",
+    assembly_pui: record.assembly_pui ?? "",
+    description: record.description ?? "",
+    is_derived: record.is_derived === true ? "true" : record.is_derived === false ? "false" : NONE_SELECT_VALUE,
+    md5checksum: record.md5checksum ?? "",
+    source_uri: record.source_uri ?? "",
+    species_ontology_term: record.species_ontology_term ?? "",
+    species_ontology_termuri: record.species_ontology_termuri ?? "",
+    source_germplasm_id: record.source_germplasm_id && record.source_germplasm_id !== NONE_SELECT_VALUE
+      ? record.source_germplasm_id
+      : NONE_SELECT_VALUE,
+  };
+}
+
+export function normalizeReferenceFormData(record: ReferenceRecord): Record<string, unknown> {
+  return {
+    id: record.id,
+    reference_name: record.reference_name ?? "",
+    reference_set_id: record.reference_set_id ?? "",
+    length: record.length ?? "",
+    md5checksum: record.md5checksum ?? "",
+    source_divergence: record.source_divergence ?? "",
+  };
+}
+
+export function normalizeReferenceBasesFormData(record: ReferenceBasesRecord): Record<string, unknown> {
+  return {
+    id: record.id,
+    reference_id: record.reference_id ?? "",
+    page_number: record.page_number ?? "",
+    bases: record.bases ?? "",
+  };
+}
+
 export async function createReferenceSetRow(payload: ReferenceSetPayload): Promise<ReferenceSetRecord> {
+  const body = {
+    ...buildReferenceSetWriteBody(payload),
+    ...(optionalText(payload.id) ? { referenceSetDbId: optionalText(payload.id) } : {}),
+  };
  const response = await request<BrapiListResponse<ReferenceSetRecord>>("/brapi/v2/referencesets", {
    method: "POST",
-    body: JSON.stringify({
-      referenceSetDbId: requiredText(payload.id, "ReferenceSet ID 不能为空"),
-      ...referenceSetBody(payload),
-    }),
+    body: JSON.stringify(body),
  });
  invalidateReferenceSetPageCache();
  return mapReferenceSet(response.result.data[0]);
@@ -313,7 +509,7 @@ export async function updateReferenceSetRow(id: string, payload: ReferenceSetPay
    `/brapi/v2/referencesets/${encodeURIComponent(id)}`,
    {
      method: "PUT",
-      body: JSON.stringify(referenceSetBody(payload)),
+      body: JSON.stringify(buildReferenceSetWriteBody(payload)),
    },
  );
  invalidateReferenceSetPageCache();
@@ -329,12 +525,13 @@ export async function deleteReferenceSetRow(id: string): Promise<void> {
 }

 export async function createReferenceRow(payload: ReferencePayload): Promise<ReferenceRecord> {
+  const body = {
+    ...buildReferenceWriteBody(payload),
+    ...(optionalText(payload.id) ? { referenceDbId: optionalText(payload.id) } : {}),
+  };
  const response = await request<BrapiListResponse<ReferenceRecord>>("/brapi/v2/references", {
    method: "POST",
-    body: JSON.stringify({
-      referenceDbId: requiredText(payload.id, "Reference ID 不能为空"),
-      ...referenceBody(payload),
-    }),
+    body: JSON.stringify(body),
  });
  invalidateReferenceSetPageCache();
  return mapReference(response.result.data[0]);
@@ -349,7 +546,7 @@ export async function updateReferenceRow(id: string, payload: ReferencePayload):
    `/brapi/v2/references/${encodeURIComponent(id)}`,
    {
      method: "PUT",
-      body: JSON.stringify(referenceBody(payload)),
+      body: JSON.stringify(buildReferenceWriteBody(payload)),
    },
  );
  invalidateReferenceSetPageCache();
@@ -365,12 +562,13 @@ export async function deleteReferenceRow(id: string): Promise<void> {
 }

 export async function createReferenceBasesRow(payload: ReferenceBasesPayload): Promise<ReferenceBasesRecord> {
+  const body = {
+    ...buildReferenceBasesWriteBody(payload, true),
+    ...(optionalText(payload.id) ? { referenceBasesDbId: optionalText(payload.id) } : {}),
+  };
  const response = await request<BrapiListResponse<ReferenceBasesRecord>>("/brapi/v2/referencebases", {
    method: "POST",
-    body: JSON.stringify({
-      referenceBasesDbId: requiredText(payload.id, "ReferenceBases ID 不能为空"),
-      ...referenceBasesBody(payload),
-    }),
+    body: JSON.stringify(body),
  });
  invalidateReferenceSetPageCache();
  return mapReferenceBases(response.result.data[0]);
@@ -385,7 +583,7 @@ export async function updateReferenceBasesRow(id: string, payload: ReferenceBase
    `/brapi/v2/referencebases/${encodeURIComponent(id)}`,
    {
      method: "PUT",
-      body: JSON.stringify(referenceBasesBody(payload)),
+      body: JSON.stringify(buildReferenceBasesWriteBody(payload, false)),
    },
  );
  invalidateReferenceSetPageCache();