labgate 0.5.31 → 0.5.32

package/dist/lib/display-mcp.js

@@ -0,0 +1,160 @@
+"use strict";
+/**
+ * LabGate Display MCP Server
+ *
+ * A Model Context Protocol server that allows Claude to render rich
+ * interactive content (markdown, tables, plots, molecular structures,
+ * DNA/protein sequences) directly in the LabGate web UI.
+ *
+ * Usage: node dist/lib/display-mcp.js [--db /path/to/display.json]
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.main = main;
+const mcp_js_1 = require("@modelcontextprotocol/sdk/server/mcp.js");
+const stdio_js_1 = require("@modelcontextprotocol/sdk/server/stdio.js");
+const zod_1 = require("zod");
+const display_store_js_1 = require("./display-store.js");
+function asText(text) {
+    return {
+        content: [{ type: 'text', text }],
+    };
+}
+function asError(text) {
+    return {
+        content: [{ type: 'text', text }],
+        isError: true,
+    };
+}
+function parseDbPathFromArgs(args) {
+    let dbPath;
+    for (let i = 0; i < args.length; i++) {
+        const arg = args[i];
+        if (arg === '--db') {
+            const next = args[i + 1];
+            if (!next)
+                throw new Error('Missing value for --db');
+            dbPath = next;
+            i++;
+            continue;
+        }
+        if (arg.startsWith('--db=')) {
+            const inline = arg.slice('--db='.length);
+            if (!inline)
+                throw new Error('Missing value for --db');
+            dbPath = inline;
+        }
+    }
+    return dbPath;
+}
+const WIDGET_TYPES = [
+    'markdown',
+    'table',
+    'plot',
+    'image',
+    'pdf',
+    'molecule',
+    'sequence',
+    'alignment',
+    'file_preview',
+    'tree',
+    'heatmap',
+    'tracks',
+    'domains',
+    'network',
+];
+async function main(args = process.argv.slice(2)) {
+    const dbPath = parseDbPathFromArgs(args);
+    if (!dbPath)
+        throw new Error('--db argument is required');
+    const store = new display_store_js_1.DisplayStore(dbPath);
+    const server = new mcp_js_1.McpServer({
+        name: 'labgate-display',
+        version: '1.0.0',
+    }, {
+        capabilities: {
+            tools: {},
+        },
+        instructions: 'LabGate display widgets. Use display_widget to render rich interactive content ' +
+            'directly in the LabGate web UI — markdown with formatting, data tables, Plotly charts, ' +
+            '3D molecular structures (PDB), PDF documents, DNA/RNA/protein sequences with coloring, ' +
+            'multiple sequence alignments, phylogenetic trees, clustered heatmaps, ' +
+            'genome feature tracks, protein domain architectures, network graphs, ' +
+            'images, and file previews. ' +
+            'The widget appears inline in the chat transcript for the researcher to interact with.',
+    });
+    // ── Tool: display_widget ──────────────────────────────
+    server.registerTool('display_widget', {
+        title: 'Display Widget',
+        description: 'Render rich interactive content in the LabGate web UI. ' +
+            'Supported widget types:\n' +
+            '- markdown: Formatted text with headings, code blocks, tables, math\n' +
+            '- table: Structured data table with sortable columns\n' +
+            '- plot: Interactive chart (Plotly.js specification)\n' +
+            '- image: Display an image from the container filesystem\n' +
+            '- pdf: PDF document viewer with page navigation\n' +
+            '- molecule: 3D molecular structure viewer (PDB ID, inline data, or file)\n' +
+            '- sequence: Colored DNA/RNA/protein sequence display\n' +
+            '- alignment: Multiple sequence alignment with conservation highlighting\n' +
+            '- file_preview: Preview of CSV, TSV, FASTA, or other data files\n' +
+            '- tree: Phylogenetic tree from Newick format string\n' +
+            '- heatmap: Clustered heatmap with optional dendrograms\n' +
+            '- tracks: Genome feature track viewer (GFF3, BED, VCF via igv.js)\n' +
+            '- domains: Protein domain/feature architecture diagram\n' +
+            '- network: Interactive network/graph visualization\n\n' +
+            'Data shapes per widget type:\n' +
+            '  markdown: { content: string }\n' +
+            '  table: { columns: string[], rows: (string|number)[][], caption?: string }\n' +
+            '  plot: { plotly: { data: PlotlyTrace[], layout?: PlotlyLayout } }\n' +
+            '  image: { path: string, alt?: string, caption?: string }\n' +
+            '  pdf: { path: string, page?: number }\n' +
+            '  molecule: { pdb_id?: string, pdb_data?: string, path?: string, style?: "cartoon"|"ball-and-stick"|"surface" }\n' +
+            '  sequence: { sequence: string, type: "dna"|"rna"|"protein", label?: string }\n' +
+            '  alignment: { sequences: { id: string, seq: string }[], format?: "clustal"|"fasta" }\n' +
+            '  file_preview: { path: string, format?: string, head_lines?: number }\n' +
+            '  tree: { newick: string, layout?: "rectangular"|"radial" }\n' +
+            '  heatmap: { matrix: number[][], row_labels?: string[], col_labels?: string[], colorscale?: "viridis"|"inferno"|"plasma"|"blues"|"reds", cluster_rows?: boolean, cluster_cols?: boolean }\n' +
+            '  tracks: { genome?: string, locus?: string, tracks: { name: string, path?: string, url?: string, format: string }[] }\n' +
+            '  domains: { length: number, label?: string, features: { type: string, name: string, start: number, end: number, color?: string }[] }\n' +
+            '  network: { nodes: { id: string, label?: string, color?: string }[], edges: { source: string, target: string, label?: string, weight?: number }[], layout?: "cose"|"circle"|"grid"|"concentric"|"breadthfirst", directed?: boolean }',
+        inputSchema: {
+            widget: zod_1.z.enum(WIDGET_TYPES).describe('Widget type to render'),
+            title: zod_1.z.string().optional().describe('Optional title displayed above the widget'),
+            data: zod_1.z.record(zod_1.z.string(), zod_1.z.unknown()).describe('Widget-specific data payload (see tool description for shapes per widget type)'),
+        },
+    }, async ({ widget, title, data }) => {
+        try {
+            // Validate payload size — reject oversized inline data
+            const payloadSize = JSON.stringify(data).length;
+            if (payloadSize > 256_000) {
+                return asError(`Widget data too large (${Math.round(payloadSize / 1024)}KB). ` +
+                    'For large files, use a path reference instead of inline data.');
+            }
+            const event = store.appendEvent({
+                widget,
+                title: title || null,
+                data: data,
+                session_id: null,
+            });
+            const label = title ? `"${title}"` : widget;
+            return asText(`Widget ${label} displayed (id: ${event.id}).`);
+        }
+        catch (err) {
+            return asError(`Failed to display widget: ${err.message}`);
+        }
+    });
+    const transport = new stdio_js_1.StdioServerTransport();
+    await server.connect(transport);
+    process.on('SIGINT', () => process.exit(0));
+    process.on('SIGTERM', () => process.exit(0));
+}
+function isDirectRun() {
+    const argv1 = process.argv[1] || '';
+    return /(?:^|\/|\\)display-mcp(?:\.bundle)?(?:\.(?:js|mjs))?$/.test(argv1);
+}
+if (isDirectRun()) {
+    main(process.argv.slice(2)).catch((err) => {
+        console.error('Display MCP server error:', err);
+        process.exit(1);
+    });
+}
+//# sourceMappingURL=display-mcp.js.map

package/dist/lib/display-mcp.js.map

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package/dist/lib/display-store.d.ts

@@ -0,0 +1,24 @@
+export interface DisplayEvent {
+    id: string;
+    widget: string;
+    title: string | null;
+    data: Record<string, unknown>;
+    session_id: string | null;
+    created_at: string;
+}
+export declare class DisplayStore {
+    private readonly dbPath;
+    constructor(dbPath: string);
+    getPath(): string;
+    appendEvent(input: {
+        widget: string;
+        title?: string | null;
+        data?: Record<string, unknown>;
+        session_id?: string | null;
+    }): DisplayEvent;
+    listEvents(sessionId?: string): DisplayEvent[];
+    clearEvents(): void;
+    private ensureFile;
+    private readFile;
+    private writeFile;
+}

package/dist/lib/display-store.js

@@ -0,0 +1,150 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.DisplayStore = void 0;
+const crypto_1 = require("crypto");
+const fs_1 = require("fs");
+const path_1 = require("path");
+const config_js_1 = require("./config.js");
+function isRenameFallbackError(err) {
+    const code = err?.code;
+    return code === 'EBUSY' || code === 'EXDEV';
+}
+function nowIso() {
+    return new Date().toISOString();
+}
+function sanitizeString(value, maxLen) {
+    if (typeof value !== 'string')
+        return '';
+    const trimmed = value.trim();
+    return trimmed.length > maxLen ? trimmed.slice(0, maxLen) : trimmed;
+}
+function sanitizeNullableString(value, maxLen) {
+    if (value === null || value === undefined)
+        return null;
+    const normalized = sanitizeString(value, maxLen);
+    return normalized || null;
+}
+class DisplayStore {
+    dbPath;
+    constructor(dbPath) {
+        this.dbPath = dbPath;
+        this.ensureFile();
+    }
+    getPath() {
+        return this.dbPath;
+    }
+    appendEvent(input) {
+        const widget = sanitizeString(input.widget, 64);
+        if (!widget)
+            throw new Error('widget type is required');
+        const file = this.readFile();
+        const event = {
+            id: (0, crypto_1.randomUUID)(),
+            widget,
+            title: sanitizeNullableString(input.title, 240),
+            data: (input.data && typeof input.data === 'object' && !Array.isArray(input.data))
+                ? input.data
+                : {},
+            session_id: sanitizeNullableString(input.session_id, 128),
+            created_at: nowIso(),
+        };
+        file.events.push(event);
+        // Keep last 200 events to prevent unbounded growth
+        if (file.events.length > 200) {
+            file.events = file.events.slice(-200);
+        }
+        this.writeFile(file);
+        return event;
+    }
+    listEvents(sessionId) {
+        const events = this.readFile().events;
+        if (sessionId) {
+            const normalized = sanitizeString(sessionId, 128);
+            return events.filter((e) => e.session_id === normalized);
+        }
+        return events;
+    }
+    clearEvents() {
+        this.writeFile({ version: 1, events: [] });
+    }
+    ensureFile() {
+        (0, config_js_1.ensurePrivateDir)((0, path_1.dirname)(this.dbPath));
+        if (!(0, fs_1.existsSync)(this.dbPath)) {
+            const initial = { version: 1, events: [] };
+            (0, fs_1.writeFileSync)(this.dbPath, JSON.stringify(initial, null, 2) + '\n', {
+                encoding: 'utf-8',
+                mode: config_js_1.PRIVATE_FILE_MODE,
+            });
+            (0, config_js_1.ensurePrivateFile)(this.dbPath);
+            return;
+        }
+        (0, config_js_1.ensurePrivateFile)(this.dbPath);
+    }
+    readFile() {
+        this.ensureFile();
+        try {
+            const raw = (0, fs_1.readFileSync)(this.dbPath, 'utf-8');
+            const parsed = JSON.parse(raw || '{}');
+            if (!parsed || typeof parsed !== 'object') {
+                return { version: 1, events: [] };
+            }
+            const rows = Array.isArray(parsed.events) ? parsed.events : [];
+            const normalized = rows
+                .filter((r) => r && typeof r === 'object')
+                .map((r) => {
+                const id = sanitizeString(r.id, 128);
+                const widget = sanitizeString(r.widget, 64);
+                if (!id || !widget)
+                    return null;
+                return {
+                    id,
+                    widget,
+                    title: sanitizeNullableString(r.title, 240),
+                    data: (r.data && typeof r.data === 'object' && !Array.isArray(r.data)) ? r.data : {},
+                    session_id: sanitizeNullableString(r.session_id, 128),
+                    created_at: sanitizeString(r.created_at, 64) || nowIso(),
+                };
+            })
+                .filter((r) => r !== null);
+            return { version: 1, events: normalized };
+        }
+        catch {
+            return { version: 1, events: [] };
+        }
+    }
+    writeFile(next) {
+        const payload = JSON.stringify(next, null, 2) + '\n';
+        const tmpPath = (0, path_1.join)((0, path_1.dirname)(this.dbPath), `.${Date.now()}.${process.pid}.${(0, crypto_1.randomUUID)()}.display.tmp`);
+        (0, fs_1.writeFileSync)(tmpPath, payload, {
+            encoding: 'utf-8',
+            mode: config_js_1.PRIVATE_FILE_MODE,
+        });
+        try {
+            (0, fs_1.renameSync)(tmpPath, this.dbPath);
+        }
+        catch (err) {
+            if (!isRenameFallbackError(err)) {
+                try {
+                    (0, fs_1.unlinkSync)(tmpPath);
+                }
+                catch { /* Best effort cleanup. */ }
+                throw err;
+            }
+            try {
+                (0, fs_1.writeFileSync)(this.dbPath, payload, {
+                    encoding: 'utf-8',
+                    mode: config_js_1.PRIVATE_FILE_MODE,
+                });
+            }
+            finally {
+                try {
+                    (0, fs_1.unlinkSync)(tmpPath);
+                }
+                catch { /* Best effort cleanup. */ }
+            }
+        }
+        (0, config_js_1.ensurePrivateFile)(this.dbPath);
+    }
+}
+exports.DisplayStore = DisplayStore;
+//# sourceMappingURL=display-store.js.map

package/dist/lib/display-store.js.map

@@ -0,0 +1 @@
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package/dist/lib/explorer-autopilot.d.ts

@@ -0,0 +1,16 @@
+import { ExplorerStore } from './explorer-store.js';
+import type { RunStatus } from './explorer-types.js';
+export interface AutopilotTickInput {
+    experiment_id: string;
+    store?: ExplorerStore;
+    random?: () => number;
+}
+export interface AutopilotTickResult {
+    did_work: boolean;
+    message: string;
+    run_id?: string;
+    status?: RunStatus;
+    score?: number;
+    is_error?: boolean;
+}
+export declare function autopilotTick(input: AutopilotTickInput): AutopilotTickResult;