feat: serve samples from the typescript server

AGENTS.md

@@ -441,22 +441,24 @@ re-exports them so its own call sites are undisturbed.
 
 **A domain's wire shapes belong in `@virtool/contracts`, not in
 `data.ts`.** What a server function returns is read by both sides, so
-`data.ts` imports those types from the package and the client feature's
-`types.ts` re-exports them (`references/types.ts` is the worked example).
-A client `types.ts` must never `import type ... from "@server/*"` — that
-points the client at the server's emitted declarations for a shape the
-server does not own, and drags a data-layer module into the browser's
-type graph to get it. `data.ts` still owns what only it uses: its
-`*Values` and `*Options` argument types, its `AppError` subclasses, and
-its row mappers.
+`data.ts` imports those types from the package and components import the
+same names straight from `@virtool/contracts` — no feature `types.ts`
+re-export (`references/types.ts` and `samples/types.ts` are the worked
+examples; each keeps only its genuinely client-only shapes). A client
+`types.ts` must never `import type ... from "@server/*"` — that points
+the client at the server's emitted declarations for a shape the server
+does not own, and drags a data-layer module into the browser's type
+graph to get it. `data.ts` still owns what only it uses: its `*Values`
+and `*Options` argument types, its `AppError` subclasses, and its row
+mappers.
 
 ### Every server function declares an authorization policy
 
 Every server function names who may call it, as middleware, from
 `@server/auth/policy`:
 
 ```ts
-export const deleteGroup = createServerFn({ method: "POST" })
+export const deleteGroupFn = createServerFn({ method: "POST" })
 	.middleware([adminRole("base")])
 	.validator(groupIdSchema)
 	.handler(async ({ context, data }) => { ... });
@@ -632,8 +634,11 @@ The basics:
   string literal unions over `enum`.
 - **JSDoc:** Every exported `type` gets a one-line `/** ... */`.
 - **Naming:** `is`/`has`/`get` for pure reads; `check`/`validate`/
-  `assert` for may-throw. Don't suffix exports with their layer
-  (`Fn`, `Core`, `Handler`, `Impl`).
+  `assert` for may-throw. A `createServerFn` export gets an `Fn` suffix
+  (`loginFn`, `getSampleFn`) — it's an RPC call, not a plain function,
+  and the suffix marks that at every call site. The domain function it
+  wraps keeps the plain name (`login`, `getSample`) and never crosses
+  the network.
 - **Comments:** Default to none. Document *why* when non-obvious, not
   *what*.
 - **Concurrency:** Independent awaits go in `Promise.all` — don't pay

apps/web/src/account/account.ts

@@ -1,6 +1,6 @@
 import { accountQueryKeys } from "@account/keys";
 import type { Account } from "@account/types";
-import { getAccount } from "@server/users/functions";
+import { getAccountFn } from "@server/users/functions";
 import { queryOptions, useQuery } from "@tanstack/react-query";
 
 /**
@@ -21,7 +21,7 @@ import { queryOptions, useQuery } from "@tanstack/react-query";
 export function accountQueryOptions() {
 	return queryOptions<Account>({
 		queryKey: accountQueryKeys.all(),
-		queryFn: () => getAccount(),
+		queryFn: () => getAccountFn(),
 	});
 }
 

apps/web/src/account/components/__tests__/AccountProfile.test.tsx

@@ -170,7 +170,7 @@ describe("<AccountProfile />", () => {
 		expect(
 			await screen.findByText("Please specify a username"),
 		).toBeInTheDocument();
-		expect(userServerFnMocks.updateAccountHandle).not.toHaveBeenCalled();
+		expect(userServerFnMocks.updateAccountHandleFn).not.toHaveBeenCalled();
 	});
 
 	it("should handle password changes", async () => {

apps/web/src/account/queries.ts

@@ -5,13 +5,13 @@ import { resetClient } from "@app/utils";
 import type { Permissions } from "@groups/types";
 import * as Sentry from "@sentry/tanstackstart-react";
 import {
-	createApiKey,
-	deleteApiKey,
-	findApiKeys,
-	updateApiKey,
+	createApiKeyFn,
+	deleteApiKeyFn,
+	findApiKeysFn,
+	updateApiKeyFn,
 } from "@server/account/functions";
 import { logoutFn } from "@server/auth/functions";
-import { updateAccountHandle } from "@server/users/functions";
+import { updateAccountHandleFn } from "@server/users/functions";
 import { useMutation, useQuery, useQueryClient } from "@tanstack/react-query";
 import type { User } from "@users/types";
 import type { ErrorResponse } from "@/types/api";
@@ -50,11 +50,11 @@ export function useUpdateHandle() {
 	const queryClient = useQueryClient();
 
 	return useMutation<
-		Awaited<ReturnType<typeof updateAccountHandle>>,
+		Awaited<ReturnType<typeof updateAccountHandleFn>>,
 		Error,
 		{ handle: string }
 	>({
-		mutationFn: ({ handle }) => updateAccountHandle({ data: { handle } }),
+		mutationFn: ({ handle }) => updateAccountHandleFn({ data: { handle } }),
 		onSuccess: () => {
 			queryClient.invalidateQueries({ queryKey: accountQueryKeys.all() });
 		},
@@ -93,7 +93,7 @@ export function useChangePassword() {
 export function useFetchApiKeys() {
 	return useQuery<ApiKey[]>({
 		queryKey: accountQueryKeys.apiKeys(),
-		queryFn: () => findApiKeys(),
+		queryFn: () => findApiKeysFn(),
 	});
 }
 
@@ -106,12 +106,12 @@ export function useCreateApiKey() {
 	const queryClient = useQueryClient();
 
 	return useMutation<
-		Awaited<ReturnType<typeof createApiKey>>,
+		Awaited<ReturnType<typeof createApiKeyFn>>,
 		Error,
 		{ name: string; permissions: Permissions }
 	>({
 		mutationFn: ({ name, permissions }) =>
-			createApiKey({ data: { name, permissions } }),
+			createApiKeyFn({ data: { name, permissions } }),
 		onSuccess: () => {
 			queryClient.invalidateQueries({ queryKey: accountQueryKeys.apiKeys() });
 		},
@@ -127,12 +127,12 @@ export function useUpdateApiKey() {
 	const queryClient = useQueryClient();
 
 	return useMutation<
-		Awaited<ReturnType<typeof updateApiKey>>,
+		Awaited<ReturnType<typeof updateApiKeyFn>>,
 		Error,
 		{ keyId: number; permissions: Permissions }
 	>({
 		mutationFn: ({ keyId, permissions }) =>
-			updateApiKey({ data: { keyId, permissions } }),
+			updateApiKeyFn({ data: { keyId, permissions } }),
 		onSuccess: () => {
 			queryClient.invalidateQueries({ queryKey: accountQueryKeys.apiKeys() });
 		},
@@ -148,7 +148,7 @@ export function useRemoveApiKey() {
 	const queryClient = useQueryClient();
 
 	return useMutation<null, Error, { keyId: number }>({
-		mutationFn: ({ keyId }) => deleteApiKey({ data: { keyId } }),
+		mutationFn: ({ keyId }) => deleteApiKeyFn({ data: { keyId } }),
 		onSuccess: () => {
 			queryClient.invalidateQueries({ queryKey: accountQueryKeys.apiKeys() });
 		},

apps/web/src/administration/components/__tests__/Banners.test.tsx

@@ -12,13 +12,13 @@ const updateMessage = vi.fn();
 const deleteMessage = vi.fn();
 
 vi.mock("@server/messages/functions", () => ({
-	findMessage: vi.fn(),
-	findMessages: (...args: unknown[]) => findMessages(...args),
-	setActiveMessage: (...args: unknown[]) => setActiveMessage(...args),
-	clearActiveMessage: (...args: unknown[]) => clearActiveMessage(...args),
-	createMessage: (...args: unknown[]) => createMessage(...args),
-	updateMessage: (...args: unknown[]) => updateMessage(...args),
-	deleteMessage: (...args: unknown[]) => deleteMessage(...args),
+	findMessageFn: vi.fn(),
+	findMessagesFn: (...args: unknown[]) => findMessages(...args),
+	setActiveMessageFn: (...args: unknown[]) => setActiveMessage(...args),
+	clearActiveMessageFn: (...args: unknown[]) => clearActiveMessage(...args),
+	createMessageFn: (...args: unknown[]) => createMessage(...args),
+	updateMessageFn: (...args: unknown[]) => updateMessage(...args),
+	deleteMessageFn: (...args: unknown[]) => deleteMessage(...args),
 }));
 
 const { default: Banners } = await import("../Banners");

apps/web/src/administration/queries.ts

@@ -3,8 +3,8 @@ import {
 	roleQueryKeys,
 	settingsQueryKeys,
 } from "@administration/keys";
-import { getSettings, updateSettings } from "@server/settings/functions";
-import { listAdministratorRoles } from "@server/users/functions";
+import { getSettingsFn, updateSettingsFn } from "@server/settings/functions";
+import { listAdministratorRolesFn } from "@server/users/functions";
 import {
 	queryOptions,
 	useMutation,
@@ -34,7 +34,7 @@ export type SettingsUpdate = {
 export function settingsQueryOptions() {
 	return queryOptions<Settings>({
 		queryKey: settingsQueryKeys.all(),
-		queryFn: () => getSettings(),
+		queryFn: () => getSettingsFn(),
 	});
 }
 
@@ -67,7 +67,7 @@ export function useUpdateSettings() {
 	const queryClient = useQueryClient();
 
 	return useMutation<Settings, ErrorResponse, SettingsUpdate>({
-		mutationFn: (update) => updateSettings({ data: update }),
+		mutationFn: (update) => updateSettingsFn({ data: update }),
 		onSuccess: () => {
 			queryClient.invalidateQueries({
 				queryKey: settingsQueryKeys.all(),
@@ -87,7 +87,7 @@ export function useUpdateSettings() {
 export function administratorRolesQueryOptions() {
 	return queryOptions({
 		queryKey: roleQueryKeys.all(),
-		queryFn: () => listAdministratorRoles(),
+		queryFn: () => listAdministratorRolesFn(),
 	});
 }
 

apps/web/src/analyses/components/Create/QuickAnalyze.tsx

@@ -1,7 +1,7 @@
 import { Dialog, DialogTitle } from "@base/Dialog";
 import QueryError from "@base/QueryError";
 import { useListHmms } from "@hmm/queries";
-import type { SampleMinimal } from "@samples/types";
+import type { SampleMinimal } from "@virtool/contracts";
 import HmmAlert from "../HmmAlert";
 import CreateAnalysisDialogContent from "./CreateAnalysisDialogContent";
 import CreateAnalysisForm from "./CreateAnalysisForm";

apps/web/src/analyses/components/Create/SelectedSamples.tsx

@@ -1,7 +1,7 @@
 import { cn } from "@app/cn";
 import Badge from "@base/Badge";
 import BoxGroupSection from "@base/BoxGroupSection";
-import type { SampleMinimal } from "@samples/types";
+import type { SampleMinimal } from "@virtool/contracts";
 import CreateAnalysisFieldTitle from "./CreateAnalysisFieldTitle";
 
 type SelectedSamplesProps = {

apps/web/src/analyses/components/Create/__tests__/CreateAnalysisForm.test.tsx

@@ -2,10 +2,10 @@ import { screen, waitFor } from "@testing-library/react";
 import userEvent from "@testing-library/user-event";
 import { mockApiCreateAnalysis } from "@tests/api/analyses";
 import { mockApiListIndexes } from "@tests/api/indexes";
-import { mockApiGetSampleDetail } from "@tests/api/samples";
 import { createFakeAnalysisMinimal } from "@tests/fake/analyses";
 import { createFakeIndexMinimal } from "@tests/fake/indexes";
 import { createFakeSample } from "@tests/fake/samples";
+import { mockGetSample } from "@tests/server-fn/samples";
 import { mockListSubtractionsShortlist } from "@tests/server-fn/subtractions";
 import { renderWithRouter } from "@tests/setup";
 import { describe, expect, it, vi } from "vitest";
@@ -23,7 +23,7 @@ async function renderForm(indexId?: number) {
 
 	mockApiListIndexes([index]);
 	mockListSubtractionsShortlist([]);
-	mockApiGetSampleDetail(sample);
+	mockGetSample(sample);
 
 	await renderWithRouter(
 		<CreateAnalysisForm

apps/web/src/analyses/components/Nuvs/NuvsViewer.tsx

@@ -1,7 +1,7 @@
 import NuvsList from "@analyses/components/Nuvs/NuvsList";
 import NuvsToolbar from "@analyses/components/Nuvs/NuvsToolbar";
 import type { FormattedNuvsAnalysis } from "@analyses/types";
-import type { Sample } from "@samples/types";
+import type { Sample } from "@virtool/contracts";
 
 type NuVsViewerProps = {
 	/** Complete Nuvs analysis details */

apps/web/src/analyses/components/Pathoscope/PathoscopeList.tsx

@@ -1,7 +1,7 @@
 import { useSortAndFilterPathoscopeHits } from "@analyses/hooks";
 import type { FormattedPathoscopeAnalysis } from "@analyses/types";
 import Accordion from "@base/Accordion";
-import type { Sample } from "@samples/types";
+import type { Sample } from "@virtool/contracts";
 import { PathoscopeItem } from "./PathoscopeItem";
 
 type PathoscopeListProps = {

apps/web/src/analyses/components/Pathoscope/PathoscopeViewer.tsx

@@ -1,7 +1,7 @@
 import { useAnalysisSearch } from "@analyses/components/AnalysisSearchContext";
 import type { FormattedPathoscopeAnalysis } from "@analyses/types";
 import Alert from "@base/Alert";
-import type { Sample } from "@samples/types";
+import type { Sample } from "@virtool/contracts";
 import { PathoscopeList } from "./PathoscopeList";
 import { AnalysisMapping } from "./PathoscopeMapping";
 import { PathoscopeToolbar } from "./PathoscopeToolbar";

apps/web/src/analyses/components/__tests__/AnalysisList.test.tsx

@@ -1,12 +1,12 @@
 import AnalysesList from "@analyses/components/AnalysisList";
 import { screen } from "@testing-library/react";
 import { mockApiGetAnalyses } from "@tests/api/analyses";
-import { mockApiGetSampleDetail } from "@tests/api/samples";
 import { createFakeAccount } from "@tests/fake/account";
 import { createFakeAnalysisMinimal } from "@tests/fake/analyses";
 import { createFakeHmmSearchResults } from "@tests/fake/hmm";
 import { createFakeSample } from "@tests/fake/samples";
 import { mockFindHmms } from "@tests/server-fn/hmm";
+import { mockGetSample } from "@tests/server-fn/samples";
 import { mockGetAccount } from "@tests/server-fn/users";
 import { at, MemoryRouter, renderWithProviders } from "@tests/setup";
 import nock from "nock";
@@ -35,7 +35,7 @@ describe("<AnalysesToolbar />", () => {
 
 	it("should show analysis creation when user is full admin", async () => {
 		mockGetAccount(createFakeAccount({ administrator_role: "full" }));
-		mockApiGetSampleDetail(sample);
+		mockGetSample(sample);
 		renderList();
 
 		expect(await screen.findByText("Create")).toBeInTheDocument();
@@ -45,7 +45,7 @@ describe("<AnalysesToolbar />", () => {
 		const account = createFakeAccount({ administrator_role: null });
 		sample.user.id = account.id;
 		mockGetAccount(account);
-		mockApiGetSampleDetail(sample);
+		mockGetSample(sample);
 		renderList();
 
 		expect(await screen.findByText("Create")).toBeInTheDocument();
@@ -54,29 +54,29 @@ describe("<AnalysesToolbar />", () => {
 	it("should show analysis creation when user is in the correct group and write is enabled", async () => {
 		const account = createFakeAccount({ administrator_role: null });
 		sample.group = at(account.groups, 0);
-		sample.group_write = true;
+		sample.groupWrite = true;
 		mockGetAccount(account);
-		mockApiGetSampleDetail(sample);
+		mockGetSample(sample);
 		renderList();
 
 		expect(await screen.findByText("Create")).toBeInTheDocument();
 	});
 
 	it("should show analysis creation when all users editing a sample is permitted", async () => {
 		const account = createFakeAccount({ administrator_role: null });
-		sample.all_write = true;
+		sample.allWrite = true;
 		mockGetAccount(account);
-		mockApiGetSampleDetail(sample);
+		mockGetSample(sample);
 		renderList();
 
 		expect(await screen.findByText("Create")).toBeInTheDocument();
 	});
 
 	it("should not render analysis creation option when user has no permissions", async () => {
-		sample.all_write = false;
-		sample.group_write = false;
+		sample.allWrite = false;
+		sample.groupWrite = false;
 		mockGetAccount(createFakeAccount({ administrator_role: null }));
-		mockApiGetSampleDetail(sample);
+		mockGetSample(sample);
 		renderList();
 
 		expect(await screen.findByText("Pathoscope")).toBeInTheDocument();