pepkio-sequence-property-calculator 0.1.0

package/README.md

@@ -0,0 +1,96 @@
+# Sequence Property Calculator
+
+Node.js ESM client and CLI for running Pepkio's sequence, dilution, and ligation calculations through one typed REST API package.
+
+# What It Does
+
+This package calls the hosted Pepkio Sequence Property Calculator from Node.js scripts, browser bundles, or CI workflows. You can submit mixed FASTA input for sequence-property analysis, run concentration dilution calculations, or compute ligation insert mass from vector and insert settings.
+
+The API runs in synchronous mode and returns structured JSON output for each run. Programmatic runs require a network connection and a Pepkio API key.
+
+# Features
+
+- Three tool modes via `mode`: `sequence`, `dilution`, `ligation`
+- Sequence mode supports multi-FASTA input with options like `mass_type`, `topology`, `strand_mode`, and `type_overrides`
+- Sequence outputs include fields such as molecular weight, GC%, pI, extinction coefficients, GRAVY, and instability index
+- Dilution mode supports `simple` and `serial` sub-modes and returns protocol steps
+- Ligation mode returns calculated `insert_mass_ng`
+- Built-in manifest helpers: `getManifest`, `listExamples`, `getExampleInput`
+- Run helpers: `run`, `getRun`, `waitForRun`
+- CLI commands: `manifest` and `run`
+
+# Installation
+
+```bash
+npm install pepkio-sequence-property-calculator
+```
+
+Requires Node.js 18 or newer.
+
+# Configuration
+
+Set an API key with `tools:run` scope before calling `run()`:
+
+```bash
+export PEPKIO_API_KEY="your-key"
+```
+
+Create a key at [Pepkio API keys](https://www.pepkio.com/account/api-keys).
+
+Optional environment variables:
+
+- `PEPKIO_API_BASE_URL` (default: `https://tools.pepkio.com`)
+- `LOCAL_PEPKIO_API_KEY` (used when base URL points to `localtest.me`)
+- `PEPKIO_SSL_VERIFY` (`0` or `false` disables TLS verification)
+
+# Quick Example
+
+```typescript
+import { PepkioClient } from "pepkio-sequence-property-calculator";
+
+const client = new PepkioClient({ apiKey: process.env.PEPKIO_API_KEY });
+
+const input = await client.getExampleInput("mixed_fasta");
+const result = await client.run(input);
+
+console.log(result.status);
+console.log(result.result?.mode);
+console.log(result.result?.valid_count);
+```
+
+# CLI
+
+```bash
+npx pepkio-sequence-property-calculator manifest --examples
+npx pepkio-sequence-property-calculator run --example mixed_fasta
+```
+
+# Typical Use Cases
+
+- Batch-check molecular properties for mixed DNA, RNA, and protein FASTA entries
+- Review protein constructs with molecular weight and pI in one API workflow
+- Run oligo property checks including GC-related outputs and extinction values
+- Plan dilution steps from stock and target concentrations
+- Calculate insert mass for cloning ligation setups
+
+# Scientific Background
+
+Sequence mode detects nucleic acid or protein input and computes properties per row. Protein pI is estimated with Bjellqvist pKa tables, and ligation mass follows the ratio-based formula used by the tool (`molarRatio * (insertLength / vectorLength) * vectorMass`). Dilution mode applies concentration-volume conversion workflows for simple and serial planning.
+
+# Web Application
+
+For researchers who prefer a graphical interface, an interactive web version is available.
+
+Web Application: https://www.pepkio.com/tools/sequence-property-calculator
+
+The web interface provides live table updates, CSV export, shareable permalinks, row-level concentration utilities, and integrated dilution and ligation tabs.
+
+# Documentation and Resources
+
+GitHub Repository: https://github.com/pepkio/pepkio-sequence-property-calculator-js
+
+Web Application: https://www.pepkio.com/tools/sequence-property-calculator
+
+# About Pepkio
+
+Pepkio (https://www.pepkio.com/) develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services (https://www.pepkio.com/cro).

package/dist/chunk-DMQJTGTY.js

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+// src/errors.ts
+var PepkioAPIError = class extends Error {
+  statusCode;
+  code;
+  details;
+  responseBody;
+  constructor(message, options) {
+    super(message);
+    this.name = "PepkioAPIError";
+    this.statusCode = options?.statusCode;
+    this.code = options?.code;
+    this.details = options?.details ?? {};
+    this.responseBody = options?.responseBody;
+  }
+  toString() {
+    const parts = [this.message];
+    if (this.code) {
+      parts.push(`code=${this.code}`);
+    }
+    if (this.statusCode !== void 0) {
+      parts.push(`status=${this.statusCode}`);
+    }
+    return parts.join(" ");
+  }
+};
+
+// src/config.ts
+var DEFAULT_API_BASE_URL = "https://tools.pepkio.com";
+var TOOL_ID = "sequence-property-calculator";
+function resolveBaseUrl(override) {
+  return (override ?? process.env.PEPKIO_API_BASE_URL ?? DEFAULT_API_BASE_URL).replace(/\/$/, "");
+}
+function resolveSslVerify(override, baseUrl) {
+  if (override !== void 0) {
+    return override;
+  }
+  const env = process.env.PEPKIO_SSL_VERIFY;
+  if (env !== void 0) {
+    return !["0", "false", "no", "off"].includes(env.trim().toLowerCase());
+  }
+  const base = baseUrl ?? resolveBaseUrl();
+  if (base.includes("localtest.me")) {
+    return false;
+  }
+  return true;
+}
+function resolveApiKey(override, baseUrl) {
+  if (override) {
+    return override;
+  }
+  const base = baseUrl ?? resolveBaseUrl();
+  if (base.includes("localtest.me")) {
+    return process.env.LOCAL_PEPKIO_API_KEY ?? process.env.PEPKIO_API_KEY;
+  }
+  return process.env.PEPKIO_API_KEY;
+}
+
+// src/types.ts
+import { z } from "zod";
+var RunResultSchema = z.object({
+  run_id: z.string(),
+  status: z.string(),
+  result: z.record(z.unknown()).nullable().optional(),
+  error: z.object({
+    code: z.string().optional(),
+    message: z.string().optional(),
+    details: z.record(z.unknown()).optional()
+  }).nullable().optional(),
+  result_url: z.string().nullable().optional(),
+  permalink: z.string().nullable().optional(),
+  duration_ms: z.number().nullable().optional()
+}).passthrough();
+function parseRunResponse(data) {
+  return RunResultSchema.parse(data);
+}
+function raiseForError(result) {
+  if (!result.error) {
+    return;
+  }
+  const err = result.error;
+  throw new PepkioAPIError(err.message ?? "Tool run failed", {
+    code: err.code,
+    responseBody: {
+      run_id: result.run_id,
+      status: result.status,
+      error: result.error
+    }
+  });
+}
+
+// src/client.ts
+import { Agent } from "undici";
+var TERMINAL_STATUSES = /* @__PURE__ */ new Set(["completed", "failed", "cancelled"]);
+var PepkioClient = class {
+  baseUrl;
+  apiKey;
+  timeoutMs;
+  verifySsl;
+  fetchFn;
+  manifest = null;
+  constructor(options = {}) {
+    this.baseUrl = resolveBaseUrl(options.baseUrl);
+    this.apiKey = resolveApiKey(options.apiKey, this.baseUrl);
+    this.timeoutMs = options.timeoutMs ?? 6e4;
+    this.verifySsl = resolveSslVerify(options.verifySsl, this.baseUrl);
+    this.fetchFn = options.fetch ?? fetch;
+  }
+  getBaseUrl() {
+    return this.baseUrl;
+  }
+  requireApiKey() {
+    if (!this.apiKey) {
+      throw new Error(
+        "API key required. Set PEPKIO_API_KEY (or LOCAL_PEPKIO_API_KEY for local), or pass apiKey to PepkioClient."
+      );
+    }
+  }
+  toolPath(suffix) {
+    return `${this.baseUrl}/api/tools/v1/tools/${TOOL_ID}${suffix}`;
+  }
+  async handleResponse(response) {
+    let body = {};
+    try {
+      const json = await response.json();
+      if (json && typeof json === "object" && !Array.isArray(json)) {
+        body = json;
+      }
+    } catch {
+      body = {};
+    }
+    if (response.ok) {
+      return body;
+    }
+    const error = body.error ?? {};
+    throw new PepkioAPIError(
+      typeof error.message === "string" ? error.message : response.statusText || "Request failed",
+      {
+        statusCode: response.status,
+        code: typeof error.code === "string" ? error.code : void 0,
+        details: error.details && typeof error.details === "object" && !Array.isArray(error.details) ? error.details : {},
+        responseBody: body
+      }
+    );
+  }
+  async request(path, init) {
+    const headers = new Headers(init?.headers);
+    if (this.apiKey) {
+      headers.set("Authorization", `Bearer ${this.apiKey}`);
+    }
+    const controller = new AbortController();
+    const timer = setTimeout(() => controller.abort(), this.timeoutMs);
+    const fetchInit = {
+      ...init,
+      headers,
+      signal: controller.signal
+    };
+    if (!this.verifySsl) {
+      fetchInit.dispatcher = new Agent({ connect: { rejectUnauthorized: false } });
+    }
+    try {
+      const response = await this.fetchFn(path, fetchInit);
+      return await this.handleResponse(response);
+    } finally {
+      clearTimeout(timer);
+    }
+  }
+  async getManifest(options) {
+    if (this.manifest !== null && !options?.refresh) {
+      return this.manifest;
+    }
+    const data = await this.request(this.toolPath("/manifest"));
+    this.manifest = data;
+    return data;
+  }
+  async listExamples() {
+    const manifest = await this.getManifest();
+    const examples = manifest.examples ?? [];
+    return examples.filter((ex) => typeof ex === "object" && ex !== null).map((ex) => ex.name).filter((name) => typeof name === "string");
+  }
+  async getExampleInput(name) {
+    const manifest = await this.getManifest();
+    for (const ex of manifest.examples ?? []) {
+      if (typeof ex === "object" && ex !== null && ex.name === name) {
+        const input = ex.input;
+        if (input && typeof input === "object" && !Array.isArray(input)) {
+          return input;
+        }
+        throw new PepkioAPIError(`Example ${JSON.stringify(name)} has no input object`);
+      }
+    }
+    throw new PepkioAPIError(`Example not found: ${JSON.stringify(name)}`);
+  }
+  async run(input, options = {}) {
+    this.requireApiKey();
+    const payload = { input };
+    const runOptions = {};
+    if (options.idempotencyKey !== void 0) {
+      runOptions.idempotency_key = options.idempotencyKey;
+    }
+    if (options.label !== void 0) {
+      runOptions.label = options.label;
+    }
+    if (Object.keys(runOptions).length > 0) {
+      payload.options = runOptions;
+    }
+    const data = await this.request(this.toolPath("/run"), {
+      method: "POST",
+      headers: { "Content-Type": "application/json" },
+      body: JSON.stringify(payload)
+    });
+    const result = parseRunResponse(data);
+    raiseForError(result);
+    return result;
+  }
+  async getRun(runId) {
+    this.requireApiKey();
+    const data = await this.request(`${this.baseUrl}/api/tools/v1/runs/${runId}`);
+    const result = parseRunResponse(data);
+    raiseForError(result);
+    return result;
+  }
+  async waitForRun(runId, options) {
+    this.requireApiKey();
+    const pollIntervalMs = options?.pollIntervalMs ?? 1e3;
+    const timeoutMs = options?.timeoutMs ?? 3e5;
+    const deadline = Date.now() + timeoutMs;
+    while (true) {
+      const result = await this.getRun(runId);
+      if (TERMINAL_STATUSES.has(result.status)) {
+        return result;
+      }
+      if (Date.now() >= deadline) {
+        throw new PepkioAPIError(
+          `Run ${runId} did not complete within ${timeoutMs}ms (status=${result.status})`,
+          { code: "TIMEOUT" }
+        );
+      }
+      await new Promise((resolve) => setTimeout(resolve, pollIntervalMs));
+    }
+  }
+};
+
+export {
+  PepkioAPIError,
+  DEFAULT_API_BASE_URL,
+  TOOL_ID,
+  resolveBaseUrl,
+  resolveApiKey,
+  parseRunResponse,
+  raiseForError,
+  PepkioClient
+};
+//# sourceMappingURL=chunk-DMQJTGTY.js.map

package/dist/chunk-DMQJTGTY.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/errors.ts","../src/config.ts","../src/types.ts","../src/client.ts"],"sourcesContent":["/** API error types. */\n\nexport class PepkioAPIError extends Error {\n  readonly statusCode?: number;\n  readonly code?: string;\n  readonly details: Record<string, unknown>;\n  readonly responseBody?: Record<string, unknown>;\n\n  constructor(\n    message: string,\n    options?: {\n      statusCode?: number;\n      code?: string;\n      details?: Record<string, unknown>;\n      responseBody?: Record<string, unknown>;\n    },\n  ) {\n    super(message);\n    this.name = \"PepkioAPIError\";\n    this.statusCode = options?.statusCode;\n    this.code = options?.code;\n    this.details = options?.details ?? {};\n    this.responseBody = options?.responseBody;\n  }\n\n  override toString(): string {\n    const parts = [this.message];\n    if (this.code) {\n      parts.push(`code=${this.code}`);\n    }\n    if (this.statusCode !== undefined) {\n      parts.push(`status=${this.statusCode}`);\n    }\n    return parts.join(\" \");\n  }\n}\n","/** Configuration and environment resolution. */\n\nexport const DEFAULT_API_BASE_URL = \"https://tools.pepkio.com\";\nexport const TOOL_ID = \"sequence-property-calculator\";\n\nexport function resolveBaseUrl(override?: string): string {\n  return (override ?? process.env.PEPKIO_API_BASE_URL ?? DEFAULT_API_BASE_URL).replace(/\\/$/, \"\");\n}\n\nexport function resolveSslVerify(override?: boolean, baseUrl?: string): boolean {\n  if (override !== undefined) {\n    return override;\n  }\n  const env = process.env.PEPKIO_SSL_VERIFY;\n  if (env !== undefined) {\n    return ![\"0\", \"false\", \"no\", \"off\"].includes(env.trim().toLowerCase());\n  }\n  const base = baseUrl ?? resolveBaseUrl();\n  if (base.includes(\"localtest.me\")) {\n    return false;\n  }\n  return true;\n}\n\nexport function resolveApiKey(override?: string, baseUrl?: string): string | undefined {\n  if (override) {\n    return override;\n  }\n  const base = baseUrl ?? resolveBaseUrl();\n  if (base.includes(\"localtest.me\")) {\n    return process.env.LOCAL_PEPKIO_API_KEY ?? process.env.PEPKIO_API_KEY;\n  }\n  return process.env.PEPKIO_API_KEY;\n}\n","/** Typed API request/response models. */\n\nimport { z } from \"zod\";\n\nimport { PepkioAPIError } from \"./errors.js\";\n\nexport const RunResultSchema = z\n  .object({\n    run_id: z.string(),\n    status: z.string(),\n    result: z.record(z.unknown()).nullable().optional(),\n    error: z\n      .object({\n        code: z.string().optional(),\n        message: z.string().optional(),\n        details: z.record(z.unknown()).optional(),\n      })\n      .nullable()\n      .optional(),\n    result_url: z.string().nullable().optional(),\n    permalink: z.string().nullable().optional(),\n    duration_ms: z.number().nullable().optional(),\n  })\n  .passthrough();\n\nexport type RunResult = z.infer<typeof RunResultSchema>;\n\nexport function parseRunResponse(data: Record<string, unknown>): RunResult {\n  return RunResultSchema.parse(data);\n}\n\nexport function raiseForError(result: RunResult): void {\n  if (!result.error) {\n    return;\n  }\n  const err = result.error;\n  throw new PepkioAPIError(err.message ?? \"Tool run failed\", {\n    code: err.code,\n    responseBody: {\n      run_id: result.run_id,\n      status: result.status,\n      error: result.error,\n    },\n  });\n}\n","/** HTTP client for the Pepkio sequence-property-calculator tool. */\n\nimport { PepkioAPIError } from \"./errors.js\";\nimport { Agent, type Dispatcher } from \"undici\";\n\nimport { TOOL_ID, resolveApiKey, resolveBaseUrl, resolveSslVerify } from \"./config.js\";\nimport { type RunResult, parseRunResponse, raiseForError } from \"./types.js\";\n\nconst TERMINAL_STATUSES = new Set([\"completed\", \"failed\", \"cancelled\"]);\n\nexport interface PepkioClientOptions {\n  apiKey?: string;\n  baseUrl?: string;\n  timeoutMs?: number;\n  verifySsl?: boolean;\n  fetch?: typeof fetch;\n}\n\nexport interface RunOptions {\n  idempotencyKey?: string;\n  label?: string;\n}\n\nexport class PepkioClient {\n  private readonly baseUrl: string;\n  private readonly apiKey: string | undefined;\n  private readonly timeoutMs: number;\n  private readonly verifySsl: boolean;\n  private readonly fetchFn: typeof fetch;\n  private manifest: Record<string, unknown> | null = null;\n\n  constructor(options: PepkioClientOptions = {}) {\n    this.baseUrl = resolveBaseUrl(options.baseUrl);\n    this.apiKey = resolveApiKey(options.apiKey, this.baseUrl);\n    this.timeoutMs = options.timeoutMs ?? 60_000;\n    this.verifySsl = resolveSslVerify(options.verifySsl, this.baseUrl);\n    this.fetchFn = options.fetch ?? fetch;\n  }\n\n  getBaseUrl(): string {\n    return this.baseUrl;\n  }\n\n  private requireApiKey(): void {\n    if (!this.apiKey) {\n      throw new Error(\n        \"API key required. Set PEPKIO_API_KEY (or LOCAL_PEPKIO_API_KEY for local), \" +\n          \"or pass apiKey to PepkioClient.\",\n      );\n    }\n  }\n\n  private toolPath(suffix: string): string {\n    return `${this.baseUrl}/api/tools/v1/tools/${TOOL_ID}${suffix}`;\n  }\n\n  private async handleResponse(response: Response): Promise<Record<string, unknown>> {\n    let body: Record<string, unknown> = {};\n    try {\n      const json = await response.json();\n      if (json && typeof json === \"object\" && !Array.isArray(json)) {\n        body = json as Record<string, unknown>;\n      }\n    } catch {\n      body = {};\n    }\n\n    if (response.ok) {\n      return body;\n    }\n\n    const error = (body.error ?? {}) as Record<string, unknown>;\n    throw new PepkioAPIError(\n      typeof error.message === \"string\" ? error.message : response.statusText || \"Request failed\",\n      {\n        statusCode: response.status,\n        code: typeof error.code === \"string\" ? error.code : undefined,\n        details:\n          error.details && typeof error.details === \"object\" && !Array.isArray(error.details)\n            ? (error.details as Record<string, unknown>)\n            : {},\n        responseBody: body,\n      },\n    );\n  }\n\n  private async request(path: string, init?: RequestInit): Promise<Record<string, unknown>> {\n    const headers = new Headers(init?.headers);\n    if (this.apiKey) {\n      headers.set(\"Authorization\", `Bearer ${this.apiKey}`);\n    }\n    const controller = new AbortController();\n    const timer = setTimeout(() => controller.abort(), this.timeoutMs);\n    const fetchInit: RequestInit & { dispatcher?: Dispatcher } = {\n      ...init,\n      headers,\n      signal: controller.signal,\n    };\n    if (!this.verifySsl) {\n      fetchInit.dispatcher = new Agent({ connect: { rejectUnauthorized: false } });\n    }\n    try {\n      const response = await this.fetchFn(path, fetchInit);\n      return await this.handleResponse(response);\n    } finally {\n      clearTimeout(timer);\n    }\n  }\n\n  async getManifest(options?: { refresh?: boolean }): Promise<Record<string, unknown>> {\n    if (this.manifest !== null && !options?.refresh) {\n      return this.manifest;\n    }\n    const data = await this.request(this.toolPath(\"/manifest\"));\n    this.manifest = data;\n    return data;\n  }\n\n  async listExamples(): Promise<string[]> {\n    const manifest = await this.getManifest();\n    const examples = (manifest.examples ?? []) as unknown[];\n    return examples\n      .filter((ex): ex is Record<string, unknown> => typeof ex === \"object\" && ex !== null)\n      .map((ex) => ex.name)\n      .filter((name): name is string => typeof name === \"string\");\n  }\n\n  async getExampleInput(name: string): Promise<Record<string, unknown>> {\n    const manifest = await this.getManifest();\n    for (const ex of (manifest.examples ?? []) as unknown[]) {\n      if (typeof ex === \"object\" && ex !== null && (ex as Record<string, unknown>).name === name) {\n        const input = (ex as Record<string, unknown>).input;\n        if (input && typeof input === \"object\" && !Array.isArray(input)) {\n          return input as Record<string, unknown>;\n        }\n        throw new PepkioAPIError(`Example ${JSON.stringify(name)} has no input object`);\n      }\n    }\n    throw new PepkioAPIError(`Example not found: ${JSON.stringify(name)}`);\n  }\n\n  async run(input: Record<string, unknown>, options: RunOptions = {}): Promise<RunResult> {\n    this.requireApiKey();\n    const payload: Record<string, unknown> = { input };\n    const runOptions: Record<string, string> = {};\n    if (options.idempotencyKey !== undefined) {\n      runOptions.idempotency_key = options.idempotencyKey;\n    }\n    if (options.label !== undefined) {\n      runOptions.label = options.label;\n    }\n    if (Object.keys(runOptions).length > 0) {\n      payload.options = runOptions;\n    }\n    const data = await this.request(this.toolPath(\"/run\"), {\n      method: \"POST\",\n      headers: { \"Content-Type\": \"application/json\" },\n      body: JSON.stringify(payload),\n    });\n    const result = parseRunResponse(data);\n    raiseForError(result);\n    return result;\n  }\n\n  async getRun(runId: string): Promise<RunResult> {\n    this.requireApiKey();\n    const data = await this.request(`${this.baseUrl}/api/tools/v1/runs/${runId}`);\n    const result = parseRunResponse(data);\n    raiseForError(result);\n    return result;\n  }\n\n  async waitForRun(\n    runId: string,\n    options?: { pollIntervalMs?: number; timeoutMs?: number },\n  ): Promise<RunResult> {\n    this.requireApiKey();\n    const pollIntervalMs = options?.pollIntervalMs ?? 1000;\n    const timeoutMs = options?.timeoutMs ?? 300_000;\n    const deadline = Date.now() + timeoutMs;\n    while (true) {\n      const result = await this.getRun(runId);\n      if (TERMINAL_STATUSES.has(result.status)) {\n        return result;\n      }\n      if (Date.now() >= deadline) {\n        throw new PepkioAPIError(\n          `Run ${runId} did not complete within ${timeoutMs}ms (status=${result.status})`,\n          { code: \"TIMEOUT\" },\n        );\n      }\n      await new Promise((resolve) => setTimeout(resolve, pollIntervalMs));\n    }\n  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package/dist/cli.d.ts

@@ -0,0 +1 @@
+#!/usr/bin/env node

package/dist/cli.js

@@ -0,0 +1,82 @@
+#!/usr/bin/env node
+import {
+  PepkioAPIError,
+  PepkioClient,
+  resolveApiKey,
+  resolveBaseUrl
+} from "./chunk-DMQJTGTY.js";
+
+// src/cli.ts
+import { Command } from "commander";
+function createClient(apiKey, baseUrl) {
+  const resolvedBase = resolveBaseUrl(baseUrl);
+  return new PepkioClient({
+    apiKey: apiKey ?? resolveApiKey(void 0, resolvedBase),
+    baseUrl: resolvedBase
+  });
+}
+var program = new Command();
+program.name("pepkio-sequence-property-calculator").description("TypeScript client for Pepkio sequence-property-calculator").option(
+  "--api-key <key>",
+  "Pepkio API key (tools:run scope); else LOCAL_PEPKIO_API_KEY or PEPKIO_API_KEY from env"
+).option(
+  "--base-url <url>",
+  "Tools API base URL (default: https://tools.pepkio.com or PEPKIO_API_BASE_URL)"
+);
+program.command("manifest").description("Fetch and print the tool manifest").option("--examples", "List example names only").action(async (opts, cmd) => {
+  const globals = cmd.parent?.opts();
+  try {
+    const client = createClient(globals.apiKey, globals.baseUrl);
+    const data = await client.getManifest();
+    if (opts.examples) {
+      const names = await client.listExamples();
+      for (const name of names) {
+        console.log(name);
+      }
+      return;
+    }
+    console.log(JSON.stringify(data, null, 2));
+  } catch (err) {
+    console.error(err instanceof Error ? err.message : String(err));
+    process.exit(1);
+  }
+});
+program.command("run").description("Run the tool and print the result JSON").option("--example <name>", "Run a named manifest example").option("--input-json <json>", "Tool input as JSON object").option("--label <label>", "Optional run label").option("--idempotency-key <key>", "Optional idempotency key").action(
+  async (opts, cmd) => {
+    const globals = cmd.parent?.opts();
+    if (Boolean(opts.example) === Boolean(opts.inputJson)) {
+      console.error("Provide exactly one of --example or --input-json");
+      process.exit(1);
+    }
+    try {
+      const client = createClient(globals.apiKey, globals.baseUrl);
+      let input;
+      if (opts.example) {
+        input = await client.getExampleInput(opts.example);
+      } else {
+        const parsed = JSON.parse(opts.inputJson ?? "{}");
+        if (!parsed || typeof parsed !== "object" || Array.isArray(parsed)) {
+          throw new Error("--input-json must be a JSON object");
+        }
+        input = parsed;
+      }
+      const result = await client.run(input, {
+        label: opts.label,
+        idempotencyKey: opts.idempotencyKey
+      });
+      console.log(JSON.stringify(result, null, 2));
+    } catch (err) {
+      if (err instanceof PepkioAPIError || err instanceof Error) {
+        console.error(err.message);
+      } else {
+        console.error(String(err));
+      }
+      process.exit(1);
+    }
+  }
+);
+program.parseAsync(process.argv).catch((err) => {
+  console.error(err instanceof Error ? err.message : String(err));
+  process.exit(1);
+});
+//# sourceMappingURL=cli.js.map

package/dist/cli.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/cli.ts"],"sourcesContent":["#!/usr/bin/env node\n/** Command-line interface for pepkio-sequence-property-calculator. */\n\nimport { Command } from \"commander\";\n\nimport { PepkioClient } from \"./client.js\";\nimport { PepkioAPIError } from \"./errors.js\";\nimport { resolveApiKey, resolveBaseUrl } from \"./config.js\";\n\nfunction createClient(apiKey?: string, baseUrl?: string): PepkioClient {\n  const resolvedBase = resolveBaseUrl(baseUrl);\n  return new PepkioClient({\n    apiKey: apiKey ?? resolveApiKey(undefined, resolvedBase),\n    baseUrl: resolvedBase,\n  });\n}\n\nconst program = new Command();\n\nprogram\n  .name(\"pepkio-sequence-property-calculator\")\n  .description(\"TypeScript client for Pepkio sequence-property-calculator\")\n  .option(\n    \"--api-key <key>\",\n    \"Pepkio API key (tools:run scope); else LOCAL_PEPKIO_API_KEY or PEPKIO_API_KEY from env\",\n  )\n  .option(\n    \"--base-url <url>\",\n    \"Tools API base URL (default: https://tools.pepkio.com or PEPKIO_API_BASE_URL)\",\n  );\n\nprogram\n  .command(\"manifest\")\n  .description(\"Fetch and print the tool manifest\")\n  .option(\"--examples\", \"List example names only\")\n  .action(async (opts: { examples?: boolean }, cmd) => {\n    const globals = cmd.parent?.opts() as { apiKey?: string; baseUrl?: string };\n    try {\n      const client = createClient(globals.apiKey, globals.baseUrl);\n      const data = await client.getManifest();\n      if (opts.examples) {\n        const names = await client.listExamples();\n        for (const name of names) {\n          console.log(name);\n        }\n        return;\n      }\n      console.log(JSON.stringify(data, null, 2));\n    } catch (err) {\n      console.error(err instanceof Error ? err.message : String(err));\n      process.exit(1);\n    }\n  });\n\nprogram\n  .command(\"run\")\n  .description(\"Run the tool and print the result JSON\")\n  .option(\"--example <name>\", \"Run a named manifest example\")\n  .option(\"--input-json <json>\", \"Tool input as JSON object\")\n  .option(\"--label <label>\", \"Optional run label\")\n  .option(\"--idempotency-key <key>\", \"Optional idempotency key\")\n  .action(\n    async (\n      opts: {\n        example?: string;\n        inputJson?: string;\n        label?: string;\n        idempotencyKey?: string;\n      },\n      cmd,\n    ) => {\n      const globals = cmd.parent?.opts() as { apiKey?: string; baseUrl?: string };\n      if (Boolean(opts.example) === Boolean(opts.inputJson)) {\n        console.error(\"Provide exactly one of --example or --input-json\");\n        process.exit(1);\n      }\n      try {\n        const client = createClient(globals.apiKey, globals.baseUrl);\n        let input: Record<string, unknown>;\n        if (opts.example) {\n          input = await client.getExampleInput(opts.example);\n        } else {\n          const parsed = JSON.parse(opts.inputJson ?? 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package/dist/index.d.ts

@@ -0,0 +1,130 @@
+import { z } from 'zod';
+
+/** Typed API request/response models. */
+
+declare const RunResultSchema: z.ZodObject<{
+    run_id: z.ZodString;
+    status: z.ZodString;
+    result: z.ZodOptional<z.ZodNullable<z.ZodRecord<z.ZodString, z.ZodUnknown>>>;
+    error: z.ZodOptional<z.ZodNullable<z.ZodObject<{
+        code: z.ZodOptional<z.ZodString>;
+        message: z.ZodOptional<z.ZodString>;
+        details: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
+    }, "strip", z.ZodTypeAny, {
+        code?: string | undefined;
+        message?: string | undefined;
+        details?: Record<string, unknown> | undefined;
+    }, {
+        code?: string | undefined;
+        message?: string | undefined;
+        details?: Record<string, unknown> | undefined;
+    }>>>;
+    result_url: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    permalink: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    duration_ms: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
+}, "passthrough", z.ZodTypeAny, z.objectOutputType<{
+    run_id: z.ZodString;
+    status: z.ZodString;
+    result: z.ZodOptional<z.ZodNullable<z.ZodRecord<z.ZodString, z.ZodUnknown>>>;
+    error: z.ZodOptional<z.ZodNullable<z.ZodObject<{
+        code: z.ZodOptional<z.ZodString>;
+        message: z.ZodOptional<z.ZodString>;
+        details: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
+    }, "strip", z.ZodTypeAny, {
+        code?: string | undefined;
+        message?: string | undefined;
+        details?: Record<string, unknown> | undefined;
+    }, {
+        code?: string | undefined;
+        message?: string | undefined;
+        details?: Record<string, unknown> | undefined;
+    }>>>;
+    result_url: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    permalink: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    duration_ms: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
+}, z.ZodTypeAny, "passthrough">, z.objectInputType<{
+    run_id: z.ZodString;
+    status: z.ZodString;
+    result: z.ZodOptional<z.ZodNullable<z.ZodRecord<z.ZodString, z.ZodUnknown>>>;
+    error: z.ZodOptional<z.ZodNullable<z.ZodObject<{
+        code: z.ZodOptional<z.ZodString>;
+        message: z.ZodOptional<z.ZodString>;
+        details: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
+    }, "strip", z.ZodTypeAny, {
+        code?: string | undefined;
+        message?: string | undefined;
+        details?: Record<string, unknown> | undefined;
+    }, {
+        code?: string | undefined;
+        message?: string | undefined;
+        details?: Record<string, unknown> | undefined;
+    }>>>;
+    result_url: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    permalink: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    duration_ms: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
+}, z.ZodTypeAny, "passthrough">>;
+type RunResult = z.infer<typeof RunResultSchema>;
+declare function parseRunResponse(data: Record<string, unknown>): RunResult;
+declare function raiseForError(result: RunResult): void;
+
+/** HTTP client for the Pepkio sequence-property-calculator tool. */
+
+interface PepkioClientOptions {
+    apiKey?: string;
+    baseUrl?: string;
+    timeoutMs?: number;
+    verifySsl?: boolean;
+    fetch?: typeof fetch;
+}
+interface RunOptions {
+    idempotencyKey?: string;
+    label?: string;
+}
+declare class PepkioClient {
+    private readonly baseUrl;
+    private readonly apiKey;
+    private readonly timeoutMs;
+    private readonly verifySsl;
+    private readonly fetchFn;
+    private manifest;
+    constructor(options?: PepkioClientOptions);
+    getBaseUrl(): string;
+    private requireApiKey;
+    private toolPath;
+    private handleResponse;
+    private request;
+    getManifest(options?: {
+        refresh?: boolean;
+    }): Promise<Record<string, unknown>>;
+    listExamples(): Promise<string[]>;
+    getExampleInput(name: string): Promise<Record<string, unknown>>;
+    run(input: Record<string, unknown>, options?: RunOptions): Promise<RunResult>;
+    getRun(runId: string): Promise<RunResult>;
+    waitForRun(runId: string, options?: {
+        pollIntervalMs?: number;
+        timeoutMs?: number;
+    }): Promise<RunResult>;
+}
+
+/** Configuration and environment resolution. */
+declare const DEFAULT_API_BASE_URL = "https://tools.pepkio.com";
+declare const TOOL_ID = "sequence-property-calculator";
+declare function resolveBaseUrl(override?: string): string;
+declare function resolveApiKey(override?: string, baseUrl?: string): string | undefined;
+
+/** API error types. */
+declare class PepkioAPIError extends Error {
+    readonly statusCode?: number;
+    readonly code?: string;
+    readonly details: Record<string, unknown>;
+    readonly responseBody?: Record<string, unknown>;
+    constructor(message: string, options?: {
+        statusCode?: number;
+        code?: string;
+        details?: Record<string, unknown>;
+        responseBody?: Record<string, unknown>;
+    });
+    toString(): string;
+}
+
+export { DEFAULT_API_BASE_URL, PepkioAPIError, PepkioClient, type PepkioClientOptions, type RunOptions, type RunResult, TOOL_ID, parseRunResponse, raiseForError, resolveApiKey, resolveBaseUrl };

package/dist/index.js

@@ -0,0 +1,21 @@
+import {
+  DEFAULT_API_BASE_URL,
+  PepkioAPIError,
+  PepkioClient,
+  TOOL_ID,
+  parseRunResponse,
+  raiseForError,
+  resolveApiKey,
+  resolveBaseUrl
+} from "./chunk-DMQJTGTY.js";
+export {
+  DEFAULT_API_BASE_URL,
+  PepkioAPIError,
+  PepkioClient,
+  TOOL_ID,
+  parseRunResponse,
+  raiseForError,
+  resolveApiKey,
+  resolveBaseUrl
+};
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":[],"sourcesContent":[],"mappings":"","names":[]}

package/package.json

@@ -0,0 +1,81 @@
+{
+  "name": "pepkio-sequence-property-calculator",
+  "version": "0.1.0",
+  "description": "Call the Pepkio Sequence Property Calculator REST API from Node.js with typed ESM imports and a CLI.",
+  "readme": "README_NPM.md",
+  "license": "MIT",
+  "author": "Pepkio Team",
+  "homepage": "https://www.pepkio.com/tools/sequence-property-calculator",
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/pepkio/pepkio-sequence-property-calculator-js.git"
+  },
+  "bugs": {
+    "url": "https://github.com/pepkio/pepkio-sequence-property-calculator-js/issues"
+  },
+  "publishConfig": {
+    "access": "public",
+    "registry": "https://registry.npmjs.org/"
+  },
+  "type": "module",
+  "keywords": [
+    "sequence",
+    "fasta",
+    "protein",
+    "dna",
+    "rna",
+    "molecular-weight",
+    "isoelectric-point",
+    "gc-content",
+    "extinction-coefficient",
+    "gravy",
+    "instability-index",
+    "ligation",
+    "dilution",
+    "concentration",
+    "sequence-property-calculator",
+    "pepkio",
+    "molecular-biology",
+    "bioinformatics",
+    "life-sciences",
+    "typescript",
+    "node",
+    "rest-api",
+    "scientific-computing"
+  ],
+  "main": "./dist/index.js",
+  "types": "./dist/index.d.ts",
+  "exports": {
+    ".": {
+      "import": "./dist/index.js",
+      "types": "./dist/index.d.ts"
+    }
+  },
+  "bin": {
+    "pepkio-sequence-property-calculator": "dist/cli.js"
+  },
+  "files": [
+    "dist"
+  ],
+  "scripts": {
+    "build": "tsup",
+    "test": "vitest run test/client.test.ts",
+    "test:integration": "vitest run test/integration.test.ts",
+    "test:all": "vitest run"
+  },
+  "engines": {
+    "node": ">=18"
+  },
+  "dependencies": {
+    "commander": "^13.1.0",
+    "undici": "^7.27.1",
+    "zod": "^3.24.2"
+  },
+  "devDependencies": {
+    "@types/node": "^22.15.3",
+    "dotenv": "^16.5.0",
+    "tsup": "^8.4.0",
+    "typescript": "^5.8.3",
+    "vitest": "^3.1.2"
+  }
+}