@rotifer/mcp-server 0.8.1 → 0.8.5

package/dist/server.js.map

@@ -1 +1 @@
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package/dist/tools.d.ts

@@ -8,7 +8,8 @@ export declare function searchGenes(args: {
     perPage?: number;
 }): Promise<GeneListResult>;
 export declare function getGeneDetail(args: {
-    id: string;
+    gene_id?: string;
+    content_hash?: string;
 }): Promise<Gene & {
     phenotype: Record<string, unknown>;
 }>;
@@ -20,7 +21,7 @@ export declare function arenaRankings(args: {
 export declare function geneStats(args: {
     gene_id: string;
 }): Promise<GeneStats & {
-    gene_id: string;
+    geneId: string;
 }>;
 export declare function leaderboard(args: {
     limit?: number;
@@ -31,13 +32,13 @@ export declare function leaderboard(args: {
 export declare function developerProfile(args: {
     username: string;
 }): Promise<DeveloperProfile>;
-export { listLocalGenes, listLocalAgents, createLocalAgent, agentRun, compileGene, runGene, initGene, scanGenes, wrapGene, testGene, publishGene } from "./local.js";
+export { listLocalGenes, listLocalAgents, createLocalAgent, agentRun, compileGene, runGene, initGene, scanGenes, wrapGene, testGene, publishGene, vgScan } from "./local.js";
 export declare function mcpStats(args: {
     days?: number;
 }): Promise<McpStatsResult>;
 export declare function geneVersions(args: {
     owner: string;
-    name: string;
+    gene_name: string;
 }): Promise<{
     versions: GeneVersionEntry[];
     count: number;
@@ -53,10 +54,10 @@ export declare function domainSuggestion(args: {
     count: number;
 }>;
 export interface AuthStatusResult {
-    logged_in: boolean;
+    isLoggedIn: boolean;
     username: string | null;
     provider: string | null;
-    expires_in_minutes: number | null;
+    expiresInMinutes: number | null;
 }
 export declare function authStatus(): AuthStatusResult;
 export interface LoginResult {
@@ -67,6 +68,7 @@ export interface LoginResult {
 }
 export declare function login(args: {
     provider?: string;
+    endpoint?: string;
 }): Promise<LoginResult>;
 export interface LogoutResult {
     success: boolean;
@@ -84,18 +86,17 @@ export declare function submitToArena(args: {
 export declare function installGeneFromCloud(args: {
     gene_id: string;
     project_root?: string;
+    force?: boolean;
 }): Promise<InstallResult>;
 export declare function compareGenes(args: {
     gene_ids: string[];
 }): Promise<{
     comparison: Array<{
-        gene_id: string;
-        gene_name: string;
+        geneId: string;
+        geneName: string;
         domain: string;
         fidelity: string;
-        fitness: number | null;
-        safety: number | null;
-        reputation_score: number | null;
+        reputationScore: number | null;
         downloads: number;
     }>;
     recommendation: string;

package/dist/tools.js

@@ -1,20 +1,29 @@
-import { listGenes, getGene, getArenaRankings, getGeneStatsRpc, getReputationLeaderboard, getDeveloperProfile, arenaSubmitCloud, installGene, listGeneVersions as listGeneVersionsCloud, getMcpStats as getMcpStatsCloud, getGeneReputation as getGeneReputationCloud, getMyReputation as getMyReputationCloud, suggestDomain as suggestDomainCloud, loadCloudConfig, } from "./cloud.js";
-import { loadCredentials, saveCredentials, clearCredentials, generateCodeVerifier, generateCodeChallenge, waitForOAuthCallback, } from "./auth.js";
+import { listGenes, getGene, getGeneByContentHash, getArenaRankings, getGeneStatsRpc, getReputationLeaderboard, getDeveloperProfile, arenaSubmitCloud, installGene, listGeneVersions as listGeneVersionsCloud, getMcpStats as getMcpStatsCloud, getGeneReputation as getGeneReputationCloud, getMyReputation as getMyReputationCloud, suggestDomain as suggestDomainCloud, loadCloudConfig, } from "./cloud.js";
+import { loadCredentials, saveCredentials, clearCredentials, generateCodeVerifier, generateCodeChallenge, startOAuthCallbackServer, } from "./auth.js";
 import { openBrowser } from "./open-browser.js";
+import { validateGeneName } from "./validate-gene-name.js";
+const SORT_ALIAS = {
+    popular: "downloads",
+    fitness: "reputation",
+};
 export async function searchGenes(args) {
+    const rpcSort = args.sort ? (SORT_ALIAS[args.sort] || args.sort) : undefined;
     return listGenes({
         query: args.query,
         domain: args.domain,
         fidelity: args.fidelity,
-        sort: args.sort,
+        sort: rpcSort,
         page: args.page || 1,
         perPage: Math.min(args.perPage || 20, 50),
     });
 }
 export async function getGeneDetail(args) {
-    if (!args.id)
-        throw new Error("Gene id is required");
-    return getGene(args.id);
+    if (args.content_hash) {
+        return getGeneByContentHash(args.content_hash);
+    }
+    if (!args.gene_id)
+        throw new Error("Either gene_id or content_hash is required. Use search_genes to find gene IDs.");
+    return getGene(args.gene_id);
 }
 export async function arenaRankings(args) {
     return getArenaRankings({
@@ -25,9 +34,9 @@ export async function arenaRankings(args) {
 }
 export async function geneStats(args) {
     if (!args.gene_id)
-        throw new Error("gene_id is required");
+        throw new Error("gene_id is required. Use search_genes to find gene IDs.");
     const stats = await getGeneStatsRpc(args.gene_id);
-    return { gene_id: args.gene_id, ...stats };
+    return { geneId: args.gene_id, ...stats };
 }
 export async function leaderboard(args) {
     const data = await getReputationLeaderboard(args.limit || 20);
@@ -35,23 +44,24 @@ export async function leaderboard(args) {
 }
 export async function developerProfile(args) {
     if (!args.username)
-        throw new Error("username is required");
+        throw new Error("username is required. Use get_leaderboard to find creator usernames.");
     return getDeveloperProfile(args.username);
 }
-export { listLocalGenes, listLocalAgents, createLocalAgent, agentRun, compileGene, runGene, initGene, scanGenes, wrapGene, testGene, publishGene } from "./local.js";
+export { listLocalGenes, listLocalAgents, createLocalAgent, agentRun, compileGene, runGene, initGene, scanGenes, wrapGene, testGene, publishGene, vgScan } from "./local.js";
 export async function mcpStats(args) {
     return getMcpStatsCloud(args.days || 7);
 }
 export async function geneVersions(args) {
-    if (!args.owner || !args.name)
-        throw new Error("owner and name are required");
-    const versions = await listGeneVersionsCloud(args.owner, args.name);
+    if (!args.owner || !args.gene_name)
+        throw new Error("owner and gene_name are required. Format: owner='username', gene_name='gene-name'.");
+    validateGeneName(args.gene_name);
+    const versions = await listGeneVersionsCloud(args.owner, args.gene_name);
     return { versions, count: versions.length };
 }
 // ── Reputation tools ──
 export async function geneReputation(args) {
     if (!args.gene_id)
-        throw new Error("gene_id is required");
+        throw new Error("gene_id is required. Use search_genes to find gene IDs.");
     return getGeneReputationCloud(args.gene_id);
 }
 export async function myReputation() {
@@ -66,14 +76,14 @@ export async function domainSuggestion(args) {
 export function authStatus() {
     const creds = loadCredentials();
     if (!creds) {
-        return { logged_in: false, username: null, provider: null, expires_in_minutes: null };
+        return { isLoggedIn: false, username: null, provider: null, expiresInMinutes: null };
     }
     const remaining = Math.max(0, Math.round((creds.expires_at - Date.now()) / 60_000));
     return {
-        logged_in: true,
+        isLoggedIn: true,
         username: creds.user.username,
         provider: creds.provider,
-        expires_in_minutes: remaining,
+        expiresInMinutes: remaining,
     };
 }
 export async function login(args) {
@@ -88,16 +98,18 @@ export async function login(args) {
     }
     const provider = (args.provider || "github");
     const config = loadCloudConfig();
-    const callbackPort = 9876;
+    if (args.endpoint)
+        config.endpoint = args.endpoint;
     const codeVerifier = generateCodeVerifier();
     const codeChallenge = generateCodeChallenge(codeVerifier);
+    const { port: callbackPort, waitForCallback } = await startOAuthCallbackServer();
     const authUrl = `${config.endpoint}/auth/v1/authorize?provider=${provider}` +
         `&redirect_to=http://localhost:${callbackPort}/callback` +
         `&code_challenge=${codeChallenge}` +
         `&code_challenge_method=S256`;
     openBrowser(authUrl);
     try {
-        const callbackResult = await waitForOAuthCallback(callbackPort);
+        const callbackResult = await waitForCallback;
         let accessToken;
         let refreshToken;
         if (callbackResult.startsWith("implicit:")) {
@@ -152,46 +164,51 @@ export function logout() {
     clearCredentials();
     return { success: true, message: `Logged out (was: ${existing.user.username} via ${existing.provider}).` };
 }
+function validateScore(name, value) {
+    const n = Number(value);
+    if (!Number.isFinite(n) || n < 0 || n > 1) {
+        throw new Error(`${name} must be a number between 0 and 1, got: ${value}`);
+    }
+    return n;
+}
 export async function submitToArena(args) {
     if (!args.gene_id)
-        throw new Error("gene_id is required");
+        throw new Error("gene_id is required. Use search_genes to find gene IDs.");
     return arenaSubmitCloud(args.gene_id, {
-        value: args.fitness_value,
-        safety_score: args.safety_score,
-        success_rate: args.success_rate,
-        latency_score: args.latency_score,
-        resource_efficiency: args.resource_efficiency,
+        value: validateScore("fitness_value", args.fitness_value),
+        safety_score: validateScore("safety_score", args.safety_score),
+        success_rate: validateScore("success_rate", args.success_rate),
+        latency_score: validateScore("latency_score", args.latency_score),
+        resource_efficiency: validateScore("resource_efficiency", args.resource_efficiency),
     });
 }
 export async function installGeneFromCloud(args) {
     if (!args.gene_id)
-        throw new Error("gene_id is required");
-    return installGene(args.gene_id, args.project_root || process.cwd());
+        throw new Error("gene_id is required. Use search_genes to find gene IDs.");
+    return installGene(args.gene_id, args.project_root || process.cwd(), args.force);
 }
 export async function compareGenes(args) {
     if (!args.gene_ids || args.gene_ids.length < 2) {
-        throw new Error("At least 2 gene_ids required for comparison");
+        throw new Error("At least 2 gene_ids required for comparison. Provide 2-5 gene UUIDs.");
     }
     if (args.gene_ids.length > 5) {
-        throw new Error("Maximum 5 genes can be compared at once");
+        throw new Error("Maximum 5 genes can be compared at once. Provide 2-5 gene UUIDs.");
     }
     const genes = await Promise.all(args.gene_ids.map((id) => getGene(id)));
     const comparison = genes.map((g) => ({
-        gene_id: g.id,
-        gene_name: g.name,
+        geneId: g.id,
+        geneName: g.name,
         domain: g.domain,
         fidelity: g.fidelity,
-        fitness: g.reputation_score,
-        safety: null,
-        reputation_score: g.reputation_score,
+        reputationScore: g.reputationScore,
         downloads: g.downloads,
     }));
-    const sorted = [...comparison].sort((a, b) => (b.reputation_score || 0) - (a.reputation_score || 0));
+    const sorted = [...comparison].sort((a, b) => (b.reputationScore || 0) - (a.reputationScore || 0));
     const best = sorted[0];
     return {
         comparison,
         recommendation: best
-            ? `Based on available metrics, "${best.gene_name}" has the highest score (${best.reputation_score ?? "N/A"}). Use Arena rankings for authoritative F(g)-based comparison within a domain.`
+            ? `Based on available metrics, "${best.geneName}" has the highest score (${best.reputationScore ?? "N/A"}). Use Arena rankings for authoritative F(g)-based comparison within a domain.`
             : "Insufficient data for recommendation.",
     };
 }

package/dist/tools.js.map

@@ -1 +1 @@
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package/dist/validate-gene-name.d.ts

@@ -0,0 +1,6 @@
+/**
+ * Validate a gene name for safe filesystem and API usage.
+ * Rejects path traversal sequences, path separators, and non-conforming names.
+ * @throws Error if the name is invalid
+ */
+export declare function validateGeneName(name: string): void;

package/dist/validate-gene-name.js

@@ -0,0 +1,25 @@
+const GENE_NAME_REGEX = /^[a-z0-9]([a-z0-9._-]*[a-z0-9])?$/;
+const MAX_GENE_NAME_LENGTH = 100;
+/**
+ * Validate a gene name for safe filesystem and API usage.
+ * Rejects path traversal sequences, path separators, and non-conforming names.
+ * @throws Error if the name is invalid
+ */
+export function validateGeneName(name) {
+    if (!name || typeof name !== "string") {
+        throw new Error("Gene name must be a non-empty string");
+    }
+    if (name.length > MAX_GENE_NAME_LENGTH) {
+        throw new Error(`Gene name exceeds ${MAX_GENE_NAME_LENGTH} characters: "${name}"`);
+    }
+    if (name.includes("..")) {
+        throw new Error(`Gene name must not contain "..": "${name}"`);
+    }
+    if (name.includes("/") || name.includes("\\") || name.includes("\0")) {
+        throw new Error(`Gene name must not contain path separators or null bytes: "${name}"`);
+    }
+    if (!GENE_NAME_REGEX.test(name)) {
+        throw new Error(`Gene name "${name}" does not match required pattern: lowercase alphanumeric, dots, hyphens, underscores. Must start and end with alphanumeric.`);
+    }
+}
+//# sourceMappingURL=validate-gene-name.js.map

package/dist/validate-gene-name.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"validate-gene-name.js","sourceRoot":"","sources":["../src/validate-gene-name.ts"],"names":[],"mappings":"AAAA,MAAM,eAAe,GAAG,mCAAmC,CAAC;AAC5D,MAAM,oBAAoB,GAAG,GAAG,CAAC;AAEjC;;;;GAIG;AACH,MAAM,UAAU,gBAAgB,CAAC,IAAY;IAC3C,IAAI,CAAC,IAAI,IAAI,OAAO,IAAI,KAAK,QAAQ,EAAE,CAAC;QACtC,MAAM,IAAI,KAAK,CAAC,sCAAsC,CAAC,CAAC;IAC1D,CAAC;IACD,IAAI,IAAI,CAAC,MAAM,GAAG,oBAAoB,EAAE,CAAC;QACvC,MAAM,IAAI,KAAK,CAAC,qBAAqB,oBAAoB,iBAAiB,IAAI,GAAG,CAAC,CAAC;IACrF,CAAC;IACD,IAAI,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC;QACxB,MAAM,IAAI,KAAK,CAAC,qCAAqC,IAAI,GAAG,CAAC,CAAC;IAChE,CAAC;IACD,IAAI,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC;QACrE,MAAM,IAAI,KAAK,CAAC,8DAA8D,IAAI,GAAG,CAAC,CAAC;IACzF,CAAC;IACD,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;QAChC,MAAM,IAAI,KAAK,CACb,cAAc,IAAI,8HAA8H,CACjJ,CAAC;IACJ,CAAC;AACH,CAAC"}

package/dist/version.d.ts

@@ -0,0 +1,8 @@
+export declare function getPackageVersion(): string;
+export interface VersionInfo {
+    current: string;
+    latest: string | null;
+    updateAvailable: boolean;
+}
+export declare function getVersionInfo(): Promise<VersionInfo>;
+export declare function formatUpdateHint(info: VersionInfo): string;

package/dist/version.js

@@ -0,0 +1,101 @@
+import { readFileSync, writeFileSync, mkdirSync, existsSync } from "node:fs";
+import { join } from "node:path";
+import { homedir } from "node:os";
+import { fileURLToPath } from "node:url";
+const __dirname = fileURLToPath(new URL(".", import.meta.url));
+const CHECK_INTERVAL_MS = 24 * 60 * 60 * 1000;
+function getConfigDir() {
+    return process.env.ROTIFER_CONFIG_DIR || join(homedir(), ".config", "rotifer");
+}
+function getCacheFile() {
+    return join(getConfigDir(), "update-check.json");
+}
+const REGISTRY_URL = "https://registry.npmjs.org";
+const FETCH_TIMEOUT_MS = 5000;
+const PKG_NAME = "@rotifer/mcp-server";
+export function getPackageVersion() {
+    const pkg = JSON.parse(readFileSync(join(__dirname, "..", "package.json"), "utf-8"));
+    return pkg.version;
+}
+function compareSemver(a, b) {
+    const pa = a.split(".").map(Number);
+    const pb = b.split(".").map(Number);
+    for (let i = 0; i < 3; i++) {
+        if ((pa[i] || 0) > (pb[i] || 0))
+            return 1;
+        if ((pa[i] || 0) < (pb[i] || 0))
+            return -1;
+    }
+    return 0;
+}
+function readCache() {
+    try {
+        const f = getCacheFile();
+        if (existsSync(f)) {
+            return JSON.parse(readFileSync(f, "utf-8"));
+        }
+    }
+    catch { /* corrupt */ }
+    return {};
+}
+function writeCache(cache) {
+    try {
+        mkdirSync(getConfigDir(), { recursive: true });
+        writeFileSync(getCacheFile(), JSON.stringify(cache, null, 2));
+    }
+    catch { /* non-critical */ }
+}
+async function fetchLatestVersion() {
+    try {
+        const controller = new AbortController();
+        const timeout = setTimeout(() => controller.abort(), FETCH_TIMEOUT_MS);
+        const res = await fetch(`${REGISTRY_URL}/${encodeURIComponent(PKG_NAME)}/latest`, {
+            signal: controller.signal,
+            headers: { accept: "application/json" },
+        });
+        clearTimeout(timeout);
+        if (!res.ok)
+            return null;
+        const data = await res.json();
+        return data.version || null;
+    }
+    catch {
+        return null;
+    }
+}
+export async function getVersionInfo() {
+    const current = getPackageVersion();
+    if (process.env.CI || process.env.NO_UPDATE_NOTIFIER || process.env.ROTIFER_NO_UPDATE_CHECK) {
+        return { current, latest: null, updateAvailable: false };
+    }
+    try {
+        const cache = readCache();
+        const entry = cache[PKG_NAME];
+        let latest = null;
+        if (entry && Date.now() - entry.lastCheck < CHECK_INTERVAL_MS) {
+            latest = entry.latest;
+        }
+        else {
+            latest = await fetchLatestVersion();
+            if (latest) {
+                cache[PKG_NAME] = { lastCheck: Date.now(), latest };
+                writeCache(cache);
+            }
+        }
+        if (!latest)
+            return { current, latest: null, updateAvailable: false };
+        return {
+            current,
+            latest,
+            updateAvailable: compareSemver(latest, current) > 0,
+        };
+    }
+    catch {
+        return { current, latest: null, updateAvailable: false };
+    }
+}
+export function formatUpdateHint(info) {
+    return `[System] Rotifer MCP Server ${info.current} → ${info.latest} update available. ` +
+        `Update with: npm i -g @rotifer/mcp-server@latest`;
+}
+//# sourceMappingURL=version.js.map

package/dist/version.js.map

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