scientify 1.0.0

package/dist/src/commands.js

@@ -0,0 +1,261 @@
+import * as fs from "node:fs";
+import * as path from "node:path";
+import * as os from "node:os";
+const WORKSPACE_ROOT = path.join(os.homedir(), ".openclaw", "workspace", "projects");
+function getActiveProject() {
+    const activePath = path.join(WORKSPACE_ROOT, ".active");
+    try {
+        return fs.readFileSync(activePath, "utf-8").trim();
+    }
+    catch {
+        return null;
+    }
+}
+function getProjectMeta(projectId) {
+    const metaPath = path.join(WORKSPACE_ROOT, projectId, "project.json");
+    try {
+        return JSON.parse(fs.readFileSync(metaPath, "utf-8"));
+    }
+    catch {
+        return null;
+    }
+}
+function listProjects() {
+    try {
+        return fs
+            .readdirSync(WORKSPACE_ROOT, { withFileTypes: true })
+            .filter((d) => d.isDirectory() && !d.name.startsWith("."))
+            .map((d) => d.name);
+    }
+    catch {
+        return [];
+    }
+}
+function formatSize(bytes) {
+    if (bytes < 1024)
+        return `${bytes}B`;
+    if (bytes < 1024 * 1024)
+        return `${(bytes / 1024).toFixed(1)}KB`;
+    return `${(bytes / (1024 * 1024)).toFixed(1)}MB`;
+}
+function getDirSize(dirPath) {
+    let size = 0;
+    try {
+        const entries = fs.readdirSync(dirPath, { withFileTypes: true });
+        for (const entry of entries) {
+            const fullPath = path.join(dirPath, entry.name);
+            if (entry.isDirectory()) {
+                size += getDirSize(fullPath);
+            }
+            else {
+                size += fs.statSync(fullPath).size;
+            }
+        }
+    }
+    catch {
+        // ignore
+    }
+    return size;
+}
+function countFiles(dirPath, pattern) {
+    let count = 0;
+    try {
+        const entries = fs.readdirSync(dirPath, { withFileTypes: true });
+        for (const entry of entries) {
+            const fullPath = path.join(dirPath, entry.name);
+            if (entry.isDirectory()) {
+                count += countFiles(fullPath, pattern);
+            }
+            else if (!pattern || pattern.test(entry.name)) {
+                count++;
+            }
+        }
+    }
+    catch {
+        // ignore
+    }
+    return count;
+}
+/**
+ * /research-status - Show workspace status
+ */
+export function handleResearchStatus(_ctx) {
+    const activeProject = getActiveProject();
+    const projects = listProjects();
+    let output = "📁 **Research Workspace Status**\n\n";
+    output += `Root: \`${WORKSPACE_ROOT}\`\n`;
+    output += `Active: ${activeProject ? `**${activeProject}**` : "(none)"}\n\n`;
+    if (projects.length === 0) {
+        output += "_No projects found. Use /idea-generation to create one._";
+    }
+    else {
+        output += "**Projects:**\n";
+        for (const proj of projects) {
+            const isActive = proj === activeProject;
+            const papersCount = countFiles(path.join(WORKSPACE_ROOT, proj, "papers"));
+            const ideasCount = countFiles(path.join(WORKSPACE_ROOT, proj, "ideas"), /\.md$/);
+            let reposCount = 0;
+            try {
+                const reposDir = path.join(WORKSPACE_ROOT, proj, "repos");
+                if (fs.existsSync(reposDir)) {
+                    reposCount = fs
+                        .readdirSync(reposDir, { withFileTypes: true })
+                        .filter((d) => d.isDirectory()).length;
+                }
+            }
+            catch {
+                // ignore
+            }
+            const marker = isActive ? "● " : "  ";
+            output += `${marker}\`${proj}\` (papers: ${papersCount}, ideas: ${ideasCount}, repos: ${reposCount})\n`;
+        }
+    }
+    return { text: output };
+}
+/**
+ * /papers - List downloaded papers
+ */
+export function handlePapers(ctx) {
+    const projectId = ctx.args?.trim() || getActiveProject();
+    if (!projectId) {
+        return { text: "❌ No active project. Use: `/papers <project-id>`" };
+    }
+    const papersDir = path.join(WORKSPACE_ROOT, projectId, "papers");
+    if (!fs.existsSync(papersDir)) {
+        return { text: `📄 **Papers in ${projectId}**\n\n_No papers directory found._` };
+    }
+    let output = `📄 **Papers in ${projectId}**\n\n`;
+    const entries = fs.readdirSync(papersDir, { withFileTypes: true });
+    let hasItems = false;
+    for (const entry of entries) {
+        if (entry.isDirectory()) {
+            const paperDir = path.join(papersDir, entry.name);
+            const texFiles = fs.readdirSync(paperDir).filter((f) => f.endsWith(".tex"));
+            output += `  [tex] \`${entry.name}\` (${texFiles.length} files)\n`;
+            hasItems = true;
+        }
+        else if (entry.name.endsWith(".pdf")) {
+            const size = formatSize(fs.statSync(path.join(papersDir, entry.name)).size);
+            output += `  [pdf] \`${entry.name.replace(".pdf", "")}\` (${size})\n`;
+            hasItems = true;
+        }
+    }
+    if (!hasItems) {
+        output += "_No papers downloaded yet._";
+    }
+    return { text: output };
+}
+/**
+ * /ideas - List generated ideas
+ */
+export function handleIdeas(ctx) {
+    const projectId = ctx.args?.trim() || getActiveProject();
+    if (!projectId) {
+        return { text: "❌ No active project. Use: `/ideas <project-id>`" };
+    }
+    const ideasDir = path.join(WORKSPACE_ROOT, projectId, "ideas");
+    if (!fs.existsSync(ideasDir)) {
+        return { text: `💡 **Ideas in ${projectId}**\n\n_No ideas directory found._` };
+    }
+    let output = `💡 **Ideas in ${projectId}**\n\n`;
+    const files = fs.readdirSync(ideasDir).filter((f) => f.endsWith(".md"));
+    if (files.length === 0) {
+        output += "_No ideas generated yet._";
+    }
+    else {
+        for (const file of files) {
+            const content = fs.readFileSync(path.join(ideasDir, file), "utf-8");
+            const titleMatch = content.match(/^#\s+(.+)$/m);
+            const title = titleMatch ? titleMatch[1] : file;
+            const isSelected = file === "selected_idea.md";
+            const marker = isSelected ? "⭐ " : "   ";
+            output += `${marker}\`${file.padEnd(22)}\` ${title}\n`;
+        }
+    }
+    return { text: output };
+}
+/**
+ * /projects - List all research projects
+ */
+export function handleProjects(_ctx) {
+    const activeProject = getActiveProject();
+    const projects = listProjects();
+    let output = "📂 **Research Projects**\n\n";
+    if (projects.length === 0) {
+        output += "_No projects found._";
+    }
+    else {
+        for (const proj of projects) {
+            const isActive = proj === activeProject;
+            const meta = getProjectMeta(proj);
+            const marker = isActive ? "● " : "  ";
+            output += `${marker}**${proj}**\n`;
+            if (meta?.name)
+                output += `    name: ${meta.name}\n`;
+            if (meta?.created)
+                output += `    created: ${meta.created}\n`;
+            if (meta?.topics?.length)
+                output += `    topics: ${meta.topics.join(", ")}\n`;
+        }
+    }
+    return { text: output };
+}
+/**
+ * /project-switch <project-id> - Switch to a different project
+ */
+export function handleProjectSwitch(ctx) {
+    const projectId = ctx.args?.trim();
+    if (!projectId) {
+        return { text: "❌ Usage: `/project-switch <project-id>`" };
+    }
+    const projectPath = path.join(WORKSPACE_ROOT, projectId);
+    if (!fs.existsSync(projectPath)) {
+        return { text: `❌ Project '${projectId}' not found.` };
+    }
+    fs.mkdirSync(WORKSPACE_ROOT, { recursive: true });
+    fs.writeFileSync(path.join(WORKSPACE_ROOT, ".active"), projectId);
+    return { text: `✓ Switched to project '**${projectId}**'` };
+}
+/**
+ * /project-delete <project-id> - Delete a research project
+ */
+export function handleProjectDelete(ctx) {
+    const projectId = ctx.args?.trim();
+    if (!projectId) {
+        return { text: "❌ Usage: `/project-delete <project-id>`" };
+    }
+    const projectPath = path.join(WORKSPACE_ROOT, projectId);
+    if (!fs.existsSync(projectPath)) {
+        return { text: `❌ Project '${projectId}' not found.` };
+    }
+    const size = formatSize(getDirSize(projectPath));
+    const papersCount = countFiles(path.join(projectPath, "papers"));
+    const ideasCount = countFiles(path.join(projectPath, "ideas"), /\.md$/);
+    // For safety, we'll return info and ask for confirmation
+    // Note: Plugin commands don't support interactive confirmation,
+    // so we provide a force flag via the args
+    if (!ctx.args?.includes("--force")) {
+        return {
+            text: `⚠️ **About to delete:**\n\n` +
+                `- Project: \`${projectId}\`\n` +
+                `- Papers: ${papersCount}\n` +
+                `- Ideas: ${ideasCount}\n` +
+                `- Size: ${size}\n\n` +
+                `To confirm, use: \`/project-delete ${projectId} --force\``,
+        };
+    }
+    // Clear active if this is the active project
+    const activeProject = getActiveProject();
+    if (activeProject === projectId) {
+        try {
+            fs.unlinkSync(path.join(WORKSPACE_ROOT, ".active"));
+        }
+        catch {
+            // ignore
+        }
+    }
+    // Delete the project directory
+    fs.rmSync(projectPath, { recursive: true, force: true });
+    return { text: `✓ Deleted project '**${projectId}**'` };
+}
+//# sourceMappingURL=commands.js.map

package/dist/src/commands.js.map

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package/dist/src/tools/arxiv-tool.d.ts

@@ -0,0 +1,26 @@
+export declare const ArxivToolSchema: import("@sinclair/typebox").TObject<{
+    query: import("@sinclair/typebox").TString;
+    max_results: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TNumber>;
+    sort_by: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
+    date_from: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
+    download: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TBoolean>;
+    output_dir: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
+}>;
+export declare function createArxivTool(): {
+    label: string;
+    name: string;
+    description: string;
+    parameters: import("@sinclair/typebox").TObject<{
+        query: import("@sinclair/typebox").TString;
+        max_results: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TNumber>;
+        sort_by: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
+        date_from: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
+        download: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TBoolean>;
+        output_dir: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
+    }>;
+    execute: (_toolCallId: string, rawArgs: unknown) => Promise<{
+        type: "tool_result";
+        content: string;
+    }>;
+};
+//# sourceMappingURL=arxiv-tool.d.ts.map

package/dist/src/tools/arxiv-tool.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"arxiv-tool.d.ts","sourceRoot":"","sources":["../../../src/tools/arxiv-tool.ts"],"names":[],"mappings":"AAUA,eAAO,MAAM,eAAe;;;;;;;EA+B1B,CAAC;AA2LH,wBAAgB,eAAe;;;;;;;;;;;;2BAOE,MAAM,WAAW,OAAO;;;;EA6ExD"}

package/dist/src/tools/arxiv-tool.js

@@ -0,0 +1,258 @@
+import { Type } from "@sinclair/typebox";
+import * as fs from "node:fs";
+import * as path from "node:path";
+import * as os from "node:os";
+import * as tar from "tar";
+const ARXIV_API_URL = "https://export.arxiv.org/api/query";
+const DEFAULT_MAX_RESULTS = 10;
+const MAX_RESULTS_LIMIT = 50;
+export const ArxivToolSchema = Type.Object({
+    query: Type.String({ description: "Search query for arXiv papers (e.g. 'graph neural network')." }),
+    max_results: Type.Optional(Type.Number({
+        description: "Maximum number of results to return (1-50). Default: 10.",
+        minimum: 1,
+        maximum: MAX_RESULTS_LIMIT,
+    })),
+    sort_by: Type.Optional(Type.String({
+        description: 'Sort order: "relevance" (default), "lastUpdatedDate", or "submittedDate".',
+    })),
+    date_from: Type.Optional(Type.String({
+        description: "Filter papers submitted after this date (YYYY-MM-DD).",
+    })),
+    download: Type.Optional(Type.Boolean({
+        description: "If true, download .tex source for each paper to output_dir. Default: false.",
+    })),
+    output_dir: Type.Optional(Type.String({
+        description: "Directory to download .tex source files into. Default: workspace/papers/",
+    })),
+});
+const SORT_MAP = {
+    relevance: "relevance",
+    lastupdateddate: "lastUpdatedDate",
+    submitteddate: "submittedDate",
+};
+function readStringParam(params, key, opts) {
+    const value = params[key];
+    if (value === undefined || value === null) {
+        if (opts?.required) {
+            throw new Error(`Missing required parameter: ${key}`);
+        }
+        return undefined;
+    }
+    return String(value);
+}
+function readNumberParam(params, key, opts) {
+    const value = params[key];
+    if (value === undefined || value === null)
+        return undefined;
+    const num = Number(value);
+    if (isNaN(num))
+        return undefined;
+    return opts?.integer ? Math.floor(num) : num;
+}
+/**
+ * Download and extract .tex source from arXiv
+ */
+async function downloadTexSource(arxivId, outputDir) {
+    const paperDir = path.join(outputDir, arxivId);
+    await fs.promises.mkdir(paperDir, { recursive: true });
+    const srcUrl = `https://arxiv.org/src/${arxivId}`;
+    const tarPath = path.join(paperDir, "source.tar.gz");
+    try {
+        // Try to download .tex source
+        const response = await fetch(srcUrl);
+        if (!response.ok) {
+            // Fallback to PDF
+            return await downloadPdfFallback(arxivId, outputDir);
+        }
+        const buffer = Buffer.from(await response.arrayBuffer());
+        await fs.promises.writeFile(tarPath, buffer);
+        // Check if it's actually a tar.gz or just a single file
+        const isTarGz = buffer[0] === 0x1f && buffer[1] === 0x8b;
+        if (isTarGz) {
+            // Extract tar.gz
+            await tar.x({ file: tarPath, cwd: paperDir });
+            await fs.promises.unlink(tarPath); // Remove tar.gz after extraction
+            // Find all .tex files
+            const files = await findTexFiles(paperDir);
+            if (files.length === 0) {
+                return await downloadPdfFallback(arxivId, outputDir);
+            }
+            return { success: true, format: "tex", files };
+        }
+        else {
+            // Single file (probably .tex directly)
+            const texPath = path.join(paperDir, "main.tex");
+            await fs.promises.rename(tarPath, texPath);
+            return { success: true, format: "tex", files: ["main.tex"] };
+        }
+    }
+    catch (error) {
+        // Fallback to PDF on any error
+        return await downloadPdfFallback(arxivId, outputDir);
+    }
+}
+async function downloadPdfFallback(arxivId, outputDir) {
+    try {
+        const pdfUrl = `https://arxiv.org/pdf/${arxivId}.pdf`;
+        const response = await fetch(pdfUrl);
+        if (!response.ok) {
+            return { success: false, format: "pdf", files: [], error: `PDF download failed: ${response.status}` };
+        }
+        const pdfPath = path.join(outputDir, `${arxivId}.pdf`);
+        const buffer = Buffer.from(await response.arrayBuffer());
+        await fs.promises.writeFile(pdfPath, buffer);
+        return { success: true, format: "pdf", files: [`${arxivId}.pdf`] };
+    }
+    catch (error) {
+        return { success: false, format: "pdf", files: [], error: String(error) };
+    }
+}
+async function findTexFiles(dir) {
+    const files = [];
+    const entries = await fs.promises.readdir(dir, { withFileTypes: true });
+    for (const entry of entries) {
+        const fullPath = path.join(dir, entry.name);
+        if (entry.isDirectory()) {
+            const subFiles = await findTexFiles(fullPath);
+            files.push(...subFiles.map((f) => path.join(entry.name, f)));
+        }
+        else if (entry.name.endsWith(".tex")) {
+            files.push(entry.name);
+        }
+    }
+    return files;
+}
+function buildSearchUrl(query, maxResults, sortBy, dateFrom) {
+    let searchQuery = query;
+    if (dateFrom) {
+        // ArXiv date filter format: submittedDate:[YYYYMMDD0000+TO+*]
+        const dateFormatted = dateFrom.replace(/-/g, "");
+        searchQuery = `${query} AND submittedDate:[${dateFormatted}0000 TO 99991231]`;
+    }
+    const params = new URLSearchParams({
+        search_query: searchQuery,
+        start: "0",
+        max_results: String(maxResults),
+        sortBy,
+        sortOrder: "descending",
+    });
+    return `${ARXIV_API_URL}?${params.toString()}`;
+}
+function parseAtomXml(xml) {
+    const papers = [];
+    const entryRegex = /<entry>([\s\S]*?)<\/entry>/g;
+    let match;
+    while ((match = entryRegex.exec(xml)) !== null) {
+        const entry = match[1];
+        const getTag = (tag) => {
+            const m = entry.match(new RegExp(`<${tag}[^>]*>([\\s\\S]*?)<\\/${tag}>`));
+            return m ? m[1].trim() : "";
+        };
+        const title = getTag("title").replace(/\s+/g, " ");
+        const abstract = getTag("summary").replace(/\s+/g, " ");
+        const published = getTag("published");
+        const updated = getTag("updated");
+        // Extract arXiv ID from <id> tag
+        const idUrl = getTag("id");
+        const arxivId = idUrl.replace("http://arxiv.org/abs/", "").replace(/v\d+$/, "");
+        // Extract authors
+        const authors = [];
+        const authorRegex = /<author>\s*<name>([^<]+)<\/name>/g;
+        let authorMatch;
+        while ((authorMatch = authorRegex.exec(entry)) !== null) {
+            authors.push(authorMatch[1].trim());
+        }
+        // Extract PDF link
+        const pdfMatch = entry.match(/<link[^>]+title="pdf"[^>]+href="([^"]+)"/);
+        const pdfUrl = pdfMatch ? pdfMatch[1] : `https://arxiv.org/pdf/${arxivId}`;
+        // Extract categories
+        const categories = [];
+        const catRegex = /<category[^>]+term="([^"]+)"/g;
+        let catMatch;
+        while ((catMatch = catRegex.exec(entry)) !== null) {
+            categories.push(catMatch[1]);
+        }
+        if (title && arxivId) {
+            papers.push({ title, authors, abstract, arxivId, pdfUrl, published, updated, categories });
+        }
+    }
+    return papers;
+}
+export function createArxivTool() {
+    return {
+        label: "ArXiv",
+        name: "arxiv",
+        description: "Search arXiv.org for academic papers by keyword. Returns titles, authors, abstracts, and IDs. Optionally downloads .tex source files.",
+        parameters: ArxivToolSchema,
+        execute: async (_toolCallId, rawArgs) => {
+            const params = rawArgs;
+            const query = readStringParam(params, "query", { required: true });
+            const maxResults = Math.min(readNumberParam(params, "max_results", { integer: true }) ?? DEFAULT_MAX_RESULTS, MAX_RESULTS_LIMIT);
+            const rawSort = readStringParam(params, "sort_by") ?? "relevance";
+            const sortBy = SORT_MAP[rawSort.toLowerCase()] ?? "relevance";
+            const dateFrom = readStringParam(params, "date_from");
+            const download = params.download === true || params.download === "true";
+            const outputDir = readStringParam(params, "output_dir") ??
+                path.join(os.homedir(), ".openclaw", "workspace", "papers");
+            const url = buildSearchUrl(query, maxResults, sortBy, dateFrom);
+            let response;
+            try {
+                response = await fetch(url);
+            }
+            catch (error) {
+                return {
+                    type: "tool_result",
+                    content: JSON.stringify({
+                        error: "network_error",
+                        message: `Failed to reach arXiv API: ${error instanceof Error ? error.message : String(error)}`,
+                    }),
+                };
+            }
+            if (!response.ok) {
+                return {
+                    type: "tool_result",
+                    content: JSON.stringify({
+                        error: "api_error",
+                        message: `arXiv API returned ${response.status}: ${response.statusText}`,
+                    }),
+                };
+            }
+            const xml = await response.text();
+            const papers = parseAtomXml(xml);
+            // If download requested, download .tex source for each paper
+            let downloads;
+            if (download && papers.length > 0) {
+                await fs.promises.mkdir(outputDir, { recursive: true });
+                downloads = [];
+                for (const paper of papers) {
+                    const result = await downloadTexSource(paper.arxivId, outputDir);
+                    downloads.push({
+                        arxiv_id: paper.arxivId,
+                        format: result.format,
+                        files: result.files,
+                        error: result.error,
+                    });
+                }
+            }
+            return {
+                type: "tool_result",
+                content: JSON.stringify({
+                    query,
+                    total: papers.length,
+                    papers: papers.map((p) => ({
+                        title: p.title,
+                        authors: p.authors,
+                        abstract: p.abstract,
+                        arxiv_id: p.arxivId,
+                        pdf_url: p.pdfUrl,
+                        published: p.published,
+                        categories: p.categories,
+                    })),
+                    ...(downloads && { downloads, output_dir: outputDir }),
+                }),
+            };
+        },
+    };
+}
+//# sourceMappingURL=arxiv-tool.js.map

package/dist/src/tools/arxiv-tool.js.map

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package/package.json

@@ -0,0 +1,47 @@
+{
+  "name": "scientify",
+  "version": "1.0.0",
+  "description": "Scientify - AI-powered research workflow automation for OpenClaw. Includes idea generation, literature review, research pipeline skills, and arxiv tool.",
+  "type": "module",
+  "main": "dist/index.js",
+  "types": "dist/index.d.ts",
+  "files": [
+    "dist",
+    "skills"
+  ],
+  "keywords": [
+    "openclaw",
+    "openclaw-plugin",
+    "research",
+    "arxiv",
+    "academic",
+    "literature-review",
+    "idea-generation"
+  ],
+  "author": "tsingyuai",
+  "license": "MIT",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/scientify/scientify"
+  },
+  "scripts": {
+    "build": "tsc",
+    "clean": "rm -rf dist",
+    "prepublishOnly": "npm run clean && npm run build"
+  },
+  "devDependencies": {
+    "openclaw": "workspace:*",
+    "@sinclair/typebox": "^0.32.0",
+    "tar": "^7.0.0",
+    "typescript": "^5.3.0",
+    "@types/node": "^20.0.0"
+  },
+  "peerDependencies": {
+    "openclaw": ">=2024.0.0"
+  },
+  "openclaw": {
+    "extensions": [
+      "./dist/index.js"
+    ]
+  }
+}