@delta-agentcloud/cli 0.0.0-stage → 1.1.22

package/scripts/install.js

@@ -0,0 +1,435 @@
+// Copyright (c) 2026 Delta Agent Cloud Authors
+// SPDX-License-Identifier: MIT
+
+const fs = require("fs");
+const path = require("path");
+const { execFileSync } = require("child_process");
+const os = require("os");
+const crypto = require("crypto");
+
+const PKG = "@delta-agentcloud/cli";
+
+// Resolve the version to download:
+//   env var > npm registry > local package.json (fallback)
+function resolveVersion() {
+  if (process.env.DELTA_CLI_VERSION) return process.env.DELTA_CLI_VERSION.replace(/^v/, "");
+  try {
+    const out = require("child_process").execFileSync("npm", ["view", PKG, "version"], {
+      stdio: ["ignore", "pipe", "pipe"],
+      timeout: 15000,
+      encoding: "utf8",
+    });
+    const ver = out.trim();
+    if (/^\d+\.\d+\.\d+/.test(ver)) return ver;
+  } catch {}
+  return require("../package.json").version.replace(/-.*$/, "");
+}
+
+const VERSION = resolveVersion();
+const NAME = "delta-cli";
+const REPO = "delta-agentcloud/delta-cli";
+const DEFAULT_ALLOWED_HOSTS = new Set([
+  "github.com",
+  "objects.githubusercontent.com",
+  "release-assets.githubusercontent.com",
+  "github-releases.githubusercontent.com",
+  "raw.githubusercontent.com",
+  "registry.npmjs.org",
+]);
+const DEFAULT_ALLOWED_HOST_PREFIXES = [
+  "github-production-release-asset-",
+];
+
+const PLATFORM_MAP = {
+  darwin: "darwin",
+  linux: "linux",
+  win32: "windows",
+};
+
+const ARCH_MAP = {
+  x64: "amd64",
+  arm64: "arm64",
+};
+
+const platform = PLATFORM_MAP[process.platform];
+const arch = ARCH_MAP[process.arch];
+
+const isWindows = process.platform === "win32";
+const ext = isWindows ? ".zip" : ".tar.gz";
+const archiveName = `${NAME}-${platform}-${arch}${ext}`;
+const GITHUB_URL = `https://github.com/${REPO}/releases/download/v${VERSION}/${archiveName}`;
+
+const binDir = path.join(__dirname, "..", "bin");
+const dest = path.join(binDir, NAME + (isWindows ? ".exe" : ""));
+
+// ── Mirror URL resolution ──────────────────────────────────────────────────
+
+var _curlTimeoutMs = null;
+
+function _getCurlTimeout() {
+  if (_curlTimeoutMs !== null) return _curlTimeoutMs;
+  var env = process.env.DELTA_CLI_DOWNLOAD_TIMEOUT;
+  var t = env ? parseInt(env, 10) : 0;
+  _curlTimeoutMs = t > 0 ? t : 60000;
+  return _curlTimeoutMs;
+}
+
+// GitHub release download mirrors.
+// Format: [hostname, urlPrefix] — urlPrefix is prepended to the GitHub URL.
+// The overseas build downloads directly from GitHub; no proxy mirrors.
+var _MIRROR_LIST = [];
+
+// A safe "discard" output path for curl. /dev/null does not exist on Windows
+// and makes curl fail with "client returned ERROR on write" (exit 23), which
+// silently broke mirror probing on Windows. Use a throwaway temp file instead.
+function discardOutputPath() {
+  if (process.platform !== "win32") return "/dev/null";
+  try {
+    return path.join(os.tmpdir(), "delta-cli-probe-" + process.pid + ".out");
+  } catch {
+    return "delta-cli-probe-" + process.pid + ".out";
+  }
+}
+
+function removeDiscardOutput(p) {
+  if (process.platform === "win32" && p) {
+    try { fs.unlinkSync(p); } catch {}
+  }
+}
+
+// Quick connectivity check: fetch a small file (checksums.txt) from each
+// mirror and return only the ones that respond within the probe timeout.
+function probeMirrors(version, cb) {
+  console.error("Probing " + _MIRROR_LIST.length + " download mirrors...");
+  var probeUrl = "/https://github.com/" + REPO + "/releases/download/v" + version + "/checksums.txt";
+  var results = [];
+  var pending = _MIRROR_LIST.length;
+  var done = false;
+
+  function finish() {
+    if (done) return;
+    done = true;
+    if (results.length > 0) {
+      console.error("Found " + results.length + " available mirror(s)");
+    } else {
+      console.error("No mirror responded, falling back to GitHub source");
+    }
+    cb(results);
+  }
+
+  if (pending === 0) return finish();
+
+  for (var i = 0; i < _MIRROR_LIST.length; i++) {
+    (function(idx) {
+      var entry = _MIRROR_LIST[idx];
+      var host = entry[0];
+      var prefix = entry[1];
+      var testUrl = prefix + probeUrl;
+      var discardPath = discardOutputPath();
+      var args = [
+        "--fail", "--location", "--silent", "--show-error",
+        "--connect-timeout", "3", "--max-time", "5",
+        "--output", discardPath, testUrl,
+      ];
+      var child;
+      try {
+        child = require("child_process").spawn("curl", args, { stdio: ["ignore", "pipe", "pipe"], timeout: 5000 });
+        var stdout = "";
+        var stderr = "";
+        child.stdout.on("data", function(d) { stdout += d; });
+        child.stderr.on("data", function(d) { stderr += d; });
+        child.on("close", function(code) {
+          removeDiscardOutput(discardPath);
+          if (code === 0) {
+            results.push(prefix + "/https://github.com/" + REPO + "/releases/download/v" + version + "/" + archiveName);
+          }
+          pending--;
+          if (pending === 0) finish();
+        });
+        child.on("error", function() {
+          removeDiscardOutput(discardPath);
+          pending--;
+          if (pending === 0) finish();
+        });
+      } catch (e) {
+        removeDiscardOutput(discardPath);
+        pending--;
+        if (pending === 0) finish();
+      }
+    })(i);
+  }
+  // Safety timeout: if probes hang, continue without mirrors after 10s
+  setTimeout(finish, 5000);
+}
+
+function releaseAssetUrls(version, assetName, cb) {
+  var urls = [];
+  var mirror = process.env.DELTA_CLI_MIRROR || "";
+  if (mirror) {
+    // The mirror proxies the full GitHub release URL by prefixing it (same
+    // scheme the probed mirrors use, e.g. https://<mirror>/https://github.com/...).
+    urls.push("" + mirror.replace(/\/$/, "") + "/https://github.com/" + REPO + "/releases/download/v" + version + "/" + assetName);
+  }
+  // Probe mirrors in parallel first, then fallback
+  probeMirrors(version, function(mirrorUrls) {
+    for (var i = 0; i < mirrorUrls.length; i++) {
+      urls.push(mirrorUrls[i]);
+    }
+    // GitHub source (last resort)
+    urls.push(GITHUB_URL);
+    cb(urls);
+  });
+}
+
+function assertAllowedHost(url) {
+  const { hostname } = new URL(url);
+  const allowlist = new Set(DEFAULT_ALLOWED_HOSTS);
+  (process.env.DELTA_CLI_MIRROR_ALLOWLIST || "")
+    .split(",")
+    .map((h) => h.trim().toLowerCase())
+    .filter(Boolean)
+    .forEach((h) => allowlist.add(h));
+  for (const allowed of allowlist) {
+    if (hostname === allowed || hostname.endsWith("." + allowed)) return;
+  }
+  for (const prefix of DEFAULT_ALLOWED_HOST_PREFIXES) {
+    if (hostname.startsWith(prefix)) return;
+  }
+  throw new Error(`Download host not allowed: ${hostname}`);
+}
+
+// ── curl version detection (for --ssl-revoke-best-effort) ──────────────────
+
+function isCurlVersionSupported(versionOutput) {
+  const match = String(versionOutput).match(/^\s*curl\s+(\d+)\.(\d+)\.(\d+)/i);
+  if (!match) return false;
+  const major = parseInt(match[1], 10);
+  const minor = parseInt(match[2], 10);
+  return major > 7 || (major === 7 && minor >= 70);
+}
+
+let _curlSupportsSslRevokeBestEffort;
+
+function curlSupportsSslRevokeBestEffort() {
+  if (_curlSupportsSslRevokeBestEffort !== undefined) {
+    return _curlSupportsSslRevokeBestEffort;
+  }
+  try {
+    const output = execFileSync("curl", ["--version"], {
+      stdio: ["ignore", "pipe", "ignore"],
+      encoding: "utf8",
+      timeout: 5000,
+    });
+    _curlSupportsSslRevokeBestEffort = isCurlVersionSupported(output);
+  } catch {
+    _curlSupportsSslRevokeBestEffort = false;
+  }
+  return _curlSupportsSslRevokeBestEffort;
+}
+
+// ── Download ───────────────────────────────────────────────────────────────
+
+function download(url, destPath) {
+  assertAllowedHost(url);
+  const args = [
+    "--fail", "--location", "--silent", "--show-error",
+    "--connect-timeout", "10",
+    "--max-time", "45",
+    "--speed-limit", "50000", "--speed-time", "10",
+    "--max-redirs", "3",
+    "--output", destPath,
+  ];
+  if (isWindows && curlSupportsSslRevokeBestEffort()) {
+    args.unshift("--ssl-revoke-best-effort");
+  }
+  args.push(url);
+  execFileSync("curl", args, { stdio: ["ignore", "ignore", "pipe"] });
+}
+
+// ── Extraction ─────────────────────────────────────────────────────────────
+
+function extractZipWindows(archivePath, destDir) {
+  const psOpts = ["-NoProfile", "-ExecutionPolicy", "Bypass", "-Command"];
+  const psEnv = {
+    DELTA_CLI_ARCHIVE: archivePath,
+    DELTA_CLI_DEST: destDir,
+  };
+  try {
+    const dotnet =
+      "$ErrorActionPreference='Stop';" +
+      "Add-Type -AssemblyName System.IO.Compression.FileSystem;" +
+      "[System.IO.Compression.ZipFile]::ExtractToDirectory($env:DELTA_CLI_ARCHIVE,$env:DELTA_CLI_DEST)";
+    execFileSync("powershell.exe", [...psOpts, dotnet], { stdio: ["ignore", "inherit", "inherit"], env: psEnv });
+  } catch (primaryErr) {
+    try {
+      const cmdlet =
+        "$ErrorActionPreference='Stop';" +
+        "Expand-Archive -LiteralPath $env:DELTA_CLI_ARCHIVE -DestinationPath $env:DELTA_CLI_DEST -Force";
+      execFileSync("powershell.exe", [...psOpts, cmdlet], { stdio: ["ignore", "inherit", "inherit"], env: psEnv });
+    } catch (secondErr) {
+      try {
+        execFileSync("tar", ["-xf", archivePath, "-C", destDir], { stdio: "ignore" });
+      } catch (fallbackErr) {
+        throw new Error(
+          `Failed to extract ${archivePath}. ` +
+          `.NET ZipFile: ${primaryErr.message}. ` +
+          `Expand-Archive: ${secondErr.message}. ` +
+          `tar: ${fallbackErr.message}`
+        );
+      }
+    }
+  }
+}
+
+// ── Checksum ───────────────────────────────────────────────────────────────
+
+function getExpectedChecksum(archiveName, checksumsDir) {
+  const dir = checksumsDir || path.join(__dirname, "..");
+  const checksumsPath = path.join(dir, "checksums.txt");
+  if (!fs.existsSync(checksumsPath)) {
+    console.error("[WARN] checksums.txt not found, skipping checksum verification");
+    return null;
+  }
+  const content = fs.readFileSync(checksumsPath, "utf8");
+  for (const line of content.split("\n")) {
+    const trimmed = line.trim();
+    if (!trimmed) continue;
+    const match = trimmed.match(/^([a-fA-F0-9]{64})\s+\*?(.+)$/);
+    if (!match) continue;
+    const hash = match[1];
+    const name = match[2];
+    if (name === archiveName) return hash;
+  }
+  throw new Error(`Checksum entry not found for ${archiveName}`);
+}
+
+function verifyChecksum(archivePath, expectedHash) {
+  if (expectedHash === null) return;
+  const hash = crypto.createHash("sha256");
+  const fd = fs.openSync(archivePath, "r");
+  try {
+    const buf = Buffer.alloc(64 * 1024);
+    let bytesRead;
+    while ((bytesRead = fs.readSync(fd, buf, 0, buf.length, null)) > 0) {
+      hash.update(buf.subarray(0, bytesRead));
+    }
+  } finally {
+    fs.closeSync(fd);
+  }
+  const actual = hash.digest("hex");
+  if (actual.toLowerCase() !== expectedHash.toLowerCase()) {
+    throw new Error(
+      `[SECURITY] Checksum mismatch for ${path.basename(archivePath)}: expected ${expectedHash} but got ${actual}`
+    );
+  }
+}
+
+// ── Main install ───────────────────────────────────────────────────────────
+
+function install() {
+  fs.mkdirSync(binDir, { recursive: true });
+  var tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), "delta-cli-"));
+  var archivePath = path.join(tmpDir, archiveName);
+
+  releaseAssetUrls(VERSION, archiveName, function(downloadUrls) {
+    try {
+      var lastErr;
+      var downloaded = false;
+      for (var i = 0; i < downloadUrls.length; i++) {
+        try {
+          console.error("Downloading from " + downloadUrls[i]);
+          download(downloadUrls[i], archivePath);
+          console.error("Download complete, verifying checksum...");
+          const expectedHash = getExpectedChecksum(archiveName);
+          verifyChecksum(archivePath, expectedHash);
+          console.error("Checksum verified");
+          downloaded = true;
+          break;
+        } catch (e) {
+          console.error("Failed: " + e.message + " (" + downloadUrls[i] + ")");
+          lastErr = e;
+        }
+      }
+      if (!downloaded) throw lastErr;
+
+      if (isWindows) {
+        console.error("Extracting archive...");
+        extractZipWindows(archivePath, tmpDir);
+      } else {
+        console.error("Extracting archive...");
+        execFileSync("tar", ["-xzf", archivePath, "-C", tmpDir], { stdio: "ignore" });
+      }
+
+      const binaryName = NAME + (isWindows ? ".exe" : "");
+      const extractedBinary = path.join(tmpDir, NAME + "-" + platform + "-" + arch);
+      if (fs.existsSync(extractedBinary)) {
+        fs.copyFileSync(extractedBinary, dest);
+      } else {
+        // Fallback: try the plain name (older release format)
+        const plainBinary = path.join(tmpDir, binaryName);
+        if (fs.existsSync(plainBinary)) {
+          fs.copyFileSync(plainBinary, dest);
+        } else {
+          // Search in tmpDir
+          const files = fs.readdirSync(tmpDir).filter(function(f) { return f.indexOf(NAME) !== -1 || f.indexOf(binaryName) !== -1; });
+          if (files.length > 0) {
+            fs.copyFileSync(path.join(tmpDir, files[0]), dest);
+          } else {
+            throw new Error("Binary not found in extracted archive. Files: " + fs.readdirSync(tmpDir).join(", "));
+          }
+        }
+      }
+      fs.chmodSync(dest, 0o755);
+      ensureExecutable(path.join(__dirname, "run.js"));
+      console.error("Installed to " + dest);
+    } finally {
+      fs.rmSync(tmpDir, { recursive: true, force: true });
+    }
+  });
+}
+
+function ensureExecutable(filePath) {
+  try {
+    if (fs.existsSync(filePath)) fs.chmodSync(filePath, 0o755);
+  } catch {}
+}
+
+// ── Entry ──────────────────────────────────────────────────────────────────
+
+if (require.main === module) {
+  if (!platform || !arch) {
+    console.error(`Unsupported platform: ${process.platform}-${process.arch}`);
+    process.exit(1);
+  }
+
+  // npx postinstall guard: skip binary download in ephemeral npx context
+  const isNpxPostinstall =
+    process.env.npm_command === "exec" && !process.env.DELTA_CLI_RUN;
+
+  if (isNpxPostinstall) {
+    process.exit(0);
+  }
+
+  try {
+    install();
+    console.log(`${NAME} v${VERSION} installed successfully`);
+  } catch (err) {
+    console.error(`Failed to install ${NAME}:`, err.message);
+    console.error(
+      `\nIf you are behind a firewall or in a restricted network, try one of:\n` +
+      `  # 1. Use a proxy:\n` +
+      `  export https_proxy=http://your-proxy:port\n` +
+      `  npm install -g ${PKG}\n\n` +
+      `  # 2. Point to a corporate npm mirror:\n` +
+      `  npm install -g ${PKG} --registry=https://your-corp-mirror/\n` +
+      `\nOr manually download from:\n` +
+      `  https://github.com/${REPO}/releases/tag/v${VERSION}`
+    );
+    process.exit(1);
+  }
+}
+
+module.exports = {
+  getExpectedChecksum, verifyChecksum, assertAllowedHost,
+  isCurlVersionSupported, curlSupportsSslRevokeBestEffort,
+};

package/scripts/run.js

@@ -0,0 +1,65 @@
+#!/usr/bin/env node
+// Copyright (c) 2026 Delta Agent Cloud Authors
+// SPDX-License-Identifier: MIT
+
+const { execFileSync } = require("child_process");
+const fs = require("fs");
+const path = require("path");
+
+const ext = process.platform === "win32" ? ".exe" : "";
+const bin = path.join(__dirname, "..", "bin", "delta-cli" + ext);
+
+// On Windows, a crashed self-update may have left the binary renamed to .old.
+const oldBin = bin + ".old";
+function restoreOldBinary() {
+  try {
+    if (fs.existsSync(bin)) {
+      fs.rmSync(bin, { force: true });
+    }
+    fs.renameSync(oldBin, bin);
+    return true;
+  } catch { return false; }
+}
+
+if (process.platform === "win32" && fs.existsSync(oldBin)) {
+  if (!fs.existsSync(bin)) {
+    restoreOldBinary();
+  } else {
+    try {
+      execFileSync(bin, ["--version"], { stdio: "ignore", timeout: 10000 });
+      try { fs.rmSync(oldBin, { force: true }); } catch {}
+    } catch {
+      restoreOldBinary();
+    }
+  }
+}
+
+const args = process.argv.slice(2);
+
+// Intercept install/uninstall — run wizard, bypass native binary
+if (args[0] === "install" || args[0] === "uninstall") {
+  require("./install-wizard.js");
+} else {
+  // Auto-download binary if missing (e.g. npx skipped postinstall)
+  if (!fs.existsSync(bin)) {
+    try {
+      execFileSync(process.execPath, [path.join(__dirname, "install.js")], {
+        stdio: "inherit",
+        env: { ...process.env, DELTA_CLI_RUN: "true", DELTA_CLI_VERSION: process.env.DELTA_CLI_VERSION || "" },
+      });
+    } catch {
+      console.error(
+        `\nFailed to auto-install delta-cli binary.\n` +
+        `To fix, run the install script manually:\n` +
+        `  node "${path.join(__dirname, "install.js")}"\n`
+      );
+      process.exit(1);
+    }
+  }
+
+  try {
+    execFileSync(bin, args, { stdio: "inherit" });
+  } catch (e) {
+    process.exit(e.status || 1);
+  }
+}

package/skills/delta-protein/AGENTS.md

@@ -0,0 +1,73 @@
+# skills/delta-protein — Protein Analysis Skill Package
+
+**Parent:** `../AGENTS.md`
+
+## OVERVIEW
+
+Single public `delta-protein` skill: the unified entry point for Huada protein and
+bioinformatics online analysis tools (mutation prediction, structure prediction, MSA,
+protein design, docking, pocket/active-site analysis, conservation/InterPro,
+enzyme kinetics, solubility/pH prediction, and PubMed/PubChem/UniProt/PISA/PLIP
+lookup). It is host-neutral and routed exclusively through the Delta CLI
+(`science invoke`) to the Science Server's `huada_protein_tools` tool. Per-endpoint
+operation contracts live in `references/` and are loaded on demand; there are no
+separate planner-visible per-tool skills and no workflow endpoints.
+
+## STRUCTURE
+
+```
+delta-protein/
+├── SKILL.md                 # single entry point: routing, CLI-only execution, safety red lines
+├── agents/
+│   └── openai.yaml          # host agent registration
+└── references/
+    └── <endpoint>.md        # one registered endpoint's operation contract
+                             #  (39 endpoints under tool `huada_protein_tools`)
+```
+
+## DATA SOURCE
+
+- Tool/endpoint identity and request fields come from the live Catalog
+  (`delta-cli science list`, `delta-cli science endpoints list <tool>`) plus the
+  authoritative parameter registry in
+  `agent/protein_common/tool_registry/definitions.py` of the `delta-search-backend`
+  project (per-tool `params`, `required_groups`, `default_params`, `timeout`).
+- Response envelope is the Huada contract `{"status","message","tool_type",
+  "resultjson","download_url"}`; per-tool `resultjson` keys are derived from the
+  tool implementations, not invented.
+- Each registered endpoint is a single tool call. Multi-step card workflows
+  (cards/*.json) are NOT registered as endpoints and are not documented here; an
+  agent may chain single endpoints in sequence when the task requires it.
+
+## CONVENTIONS
+
+- JSON/query operations go through `delta-cli science invoke --tool huada_protein_tools --endpoint <name>`; binary artifacts from `download_url` go through `delta-cli science file download`
+- Endpoint names are exact server contracts, read from the Catalog — never invent fields/enums from memory
+- Success is reported only when the subprocess exit is 0 AND top-level JSON `ok` is `true`; `data` holds the service response
+- `references/` contains only registered real endpoints; routing and tool selection belong in `SKILL.md`
+- Host-neutral: `delta-cli` is the sole service boundary; no host-specific tool/env dependencies
+- Discover newly-deployed endpoints via `delta-cli science endpoints list huada_protein_tools`
+
+## MAINTENANCE
+
+- `scripts/gen_references.py` regenerates the `## Output Projection` and
+  `## Output Template` sections in every reference from
+  `scripts/output_metadata.json` (single source of truth for field projection /
+  presentation form / downstream reuse / provenance marker). Stdlib only, idempotent.
+- Workflow: update `output_metadata.json` → run
+  `python scripts/gen_references.py` → run `python scripts/gen_references.py --check`.
+  `--check` fails loudly on missing sections, drifting titles, broken SKILL links or
+  references not covered by metadata.
+- `output_metadata.json` `provenance` is `tested` (verified by a real `delta-cli`
+  invocation) or `derived` (from ToolSpec descriptions / agent templates, marked
+  "pending live calibration"). Newly verified endpoints should be flipped to `tested`.
+- After changing references/SKILL, resync the opencode install dir:
+  `python scripts/gen_references.py --sync "%USERPROFILE%\.config\opencode\skills\delta-protein"`.
+
+## ANTI-PATTERNS
+
+- Do not call `curl`/`requests`/`httpx`/browser/PowerShell web directly against any Huada or Gateway URL
+- Do not bypass delta-cli or attach local MCP tool servers directly
+- Do not fabricate protein sequences, structures, activity data, or algorithm results, and do not pass local-library results off as Science results
+- Do not create extra JSON/CSV/report/image artifacts unless the user explicitly asks
+- Do not break relative links between SKILL.md and `references/`