omnibiofex 4.0.0 → 4.2.0

package/bin/obx

@@ -46,6 +46,21 @@ program.command('hypothesis').description('Generate hypotheses').argument('<topi
 const { timeline } = require('../src/commands/timeline');
 program.command('timeline').description('Research timeline').argument('<topic>').action(timeline);
 
+// ==================== DIAGRAM COMMAND ====================
+const { diagram } = require('../src/commands/diagram');
+
+program
+  .command('diagram')
+  .description('📊 Generate ASCII research ecosystem diagrams')
+  .argument('<topic>', 'Research topic')
+  .option('--style <style>', 'Diagram style: minimal, detailed, flowchart, network', 'detailed')
+  .option('--save', 'Save diagram to file')
+  .option('--publish', 'Save and prepare for publishing')
+  .action(async (topic, options) => {
+    await diagram(topic, options);
+  });
+
+// ==================== DATA COMMANDS ====================
 const { dataset, code } = require('../src/commands/data');
 program.command('dataset').description('Analyze dataset').argument('<file>').action(dataset);
 program.command('code').description('Review code').argument('[directory]', '.').action(code);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "omnibiofex",
-  "version": "4.0.0",
+  "version": "4.2.0",
   "description": "OmniBioFex X - The Autonomous Research Operating System",
   "main": "bin/obx",
   "bin": {

package/src/commands/diagram.js

@@ -0,0 +1,305 @@
+const chalk = require('chalk');
+const fs = require('fs');
+const path = require('path');
+const os = require('os');
+const { getAuthToken, isAuthenticated } = require('../auth');
+const { PremiumSpinner, sleep } = require('../utils/display');
+
+const BACKEND_URL = 'https://obxvisionassistant-yyedhmslhq-uc.a.run.app';
+const DIAGRAMS_DIR = path.join(os.homedir(), 'obx-diagrams');
+
+// Ensure diagrams directory exists
+if (!fs.existsSync(DIAGRAMS_DIR)) {
+  fs.mkdirSync(DIAGRAMS_DIR, { recursive: true });
+}
+
+// Diagram styles with costs
+const STYLES = {
+  minimal: { name: 'Minimal', cost: 50, description: 'Clean, simple flowchart' },
+  detailed: { name: 'Detailed', cost: 80, description: 'Comprehensive ecosystem' },
+  flowchart: { name: 'Flowchart', cost: 60, description: 'Step-by-step process' },
+  network: { name: 'Network', cost: 70, description: 'Interconnected nodes' }
+};
+
+// Generate ASCII banner
+function banner(title, width = 80) {
+  const top = `╔${'═'.repeat(width)}╗`;
+  const bottom = `╚${'═'.repeat(width)}╝`;
+  const padding = Math.max(0, width - title.length - 2);
+  const leftPad = Math.floor(padding / 2);
+  const rightPad = padding - leftPad;
+  const content = `║ ${' '.repeat(leftPad)}${title}${' '.repeat(rightPad)} ║`;
+  return `${top}\n${content}\n${bottom}`;
+}
+
+// Generate node box
+function node(text, width = 20) {
+  const safeText = text.substring(0, width - 2);
+  const padding = Math.max(0, width - safeText.length - 2);
+  const leftPad = Math.floor(padding / 2);
+  const rightPad = padding - leftPad;
+  const top = `┌${'─'.repeat(width)}┐`;
+  const bottom = `└${'─'.repeat(width)}┘`;
+  const content = `│ ${' '.repeat(leftPad)}${safeText}${' '.repeat(rightPad)} │`;
+  return `${top}\n${content}\n${bottom}`;
+}
+
+// Generate arrow
+function arrow(direction = 'down') {
+  switch (direction) {
+    case 'down': return '│\n▼';
+    case 'right': return '───▶';
+    case 'left': return '◀───';
+    case 'up': return '▲\n│';
+    default: return '│\n▼';
+  }
+}
+
+// Generate detailed diagram
+function generateDetailedDiagram(topic, data) {
+  const width = 80;
+  let diagram = banner(`${topic.toUpperCase()} RESEARCH ECOSYSTEM`, width) + '\n\n';
+  
+  // Problem identification
+  diagram += `${' '.repeat(25)}${node('Research Problem', 25)}\n`;
+  diagram += `${' '.repeat(37)}${arrow('down')}\n\n`;
+  
+  // Three input sources
+  const sources = data.components?.slice(0, 3) || ['Literature', 'Data', 'Theory'];
+  diagram += `${' '.repeat(5)}${node(sources[0] || 'Literature', 18)}     ${node(sources[1] || 'Data', 18)}     ${node(sources[2] || 'Theory', 18)}\n`;
+  diagram += `${' '.repeat(14)}\\         |         /\n`;
+  diagram += `${' '.repeat(15)}\\        |        /\n`;
+  diagram += `${' '.repeat(16)}\\       |       /\n`;
+  diagram += `${' '.repeat(17)}▼      ▼      ▼\n`;
+  diagram += `${' '.repeat(15)}${node('Integration Layer', 30)}\n`;
+  diagram += `${' '.repeat(29)}${arrow('down')}\n`;
+  
+  // Analysis phase
+  diagram += `${' '.repeat(20)}${node('Analysis Phase', 25)}\n`;
+  diagram += `${' '.repeat(32)}${arrow('down')}\n\n`;
+  
+  // Four analysis types
+  const methods = data.methods?.slice(0, 4) || ['Statistical', 'Qualitative', 'Comparative', 'Predictive'];
+  diagram += `${node(methods[0], 14)}  ${node(methods[1], 14)}  ${node(methods[2], 14)}  ${node(methods[3], 14)}\n`;
+  diagram += `${' '.repeat(7)}\\        |        |        /\n`;
+  diagram += `${' '.repeat(8)}\\       |        |       /\n`;
+  diagram += `${' '.repeat(9)}\\      |        |      /\n`;
+  diagram += `${' '.repeat(10)}▼     ▼        ▼     ▼\n`;
+  diagram += `${' '.repeat(15)}${node('Synthesis & Insights', 35)}\n`;
+  diagram += `${' '.repeat(32)}${arrow('down')}\n`;
+  
+  // Output phase
+  diagram += `${' '.repeat(20)}${node('Output Phase', 25)}\n`;
+  diagram += `${' '.repeat(32)}${arrow('down')}\n\n`;
+  
+  // Three outputs
+  const outputs = data.outputs?.slice(0, 3) || ['Publication', 'Implementation', 'Future Work'];
+  diagram += `${node(outputs[0], 18)}     ${node(outputs[1], 18)}     ${node(outputs[2], 18)}\n`;
+  
+  return diagram;
+}
+
+// Generate minimal diagram
+function generateMinimalDiagram(topic, data) {
+  const width = 60;
+  let diagram = banner(topic.toUpperCase(), width) + '\n\n';
+  
+  diagram += `${' '.repeat(20)}${node('Problem', 20)}\n`;
+  diagram += `${' '.repeat(29)}${arrow('down')}\n`;
+  diagram += `${' '.repeat(10)}${node('Research', 20)}\n`;
+  diagram += `${' '.repeat(19)}${arrow('down')}\n`;
+  diagram += `${' '.repeat(10)}${node('Analysis', 20)}\n`;
+  diagram += `${' '.repeat(19)}${arrow('down')}\n`;
+  diagram += `${' '.repeat(10)}${node('Solution', 20)}\n`;
+  
+  return diagram;
+}
+
+// Generate flowchart diagram
+function generateFlowchartDiagram(topic, data) {
+  const width = 60;
+  const steps = data.steps?.length > 0 ? data.steps : ['Research', 'Analysis', 'Implementation'];
+  let diagram = banner(`${topic.toUpperCase()} WORKFLOW`, width) + '\n\n';
+  
+  steps.forEach((step, i) => {
+    const stepText = `Step ${i + 1}: ${step}`;
+    diagram += `${' '.repeat(15)}${node(stepText, 45)}\n`;
+    if (i < steps.length - 1) {
+      diagram += `${' '.repeat(37)}${arrow('down')}\n`;
+    }
+  });
+  
+  diagram += `\n${' '.repeat(25)}${node('✓ Complete', 20)}\n`;
+  return diagram;
+}
+
+// Generate network diagram
+function generateNetworkDiagram(topic, data) {
+  const width = 70;
+  const nodes = data.nodes?.slice(0, 3) || ['Component A', 'Component B', 'Component C'];
+  let diagram = banner(`${topic.toUpperCase()} NETWORK`, width) + '\n\n';
+  
+  diagram += `${' '.repeat(25)}${node(topic, 25)}\n`;
+  diagram += `${' '.repeat(37)}|\n`;
+  diagram += `${' '.repeat(20)}┌────────┼────────┐\n`;
+  diagram += `${' '.repeat(20)}│        │        │\n`;
+  diagram += `${' '.repeat(20)}▼        ▼        ▼\n`;
+  diagram += `${node(nodes[0], 18)}  ${node(nodes[1], 18)}  ${node(nodes[2], 18)}\n`;
+  diagram += `${' '.repeat(9)}│        │        │\n`;
+  diagram += `${' '.repeat(9)}└────────┼────────┘\n`;
+  diagram += `${' '.repeat(18)}▼\n`;
+  diagram += `${' '.repeat(15)}${node('Integration', 25)}\n`;
+  
+  return diagram;
+}
+
+// Main diagram command
+async function diagram(topic, options = {}) {
+  if (!isAuthenticated()) {
+    console.error(chalk.red('✗ Not authenticated. Please run: obx login'));
+    process.exit(1);
+    return;
+  }
+
+  if (!topic) {
+    console.error(chalk.red('✗ Please provide a topic'));
+    console.log(chalk.gray('Usage: obx diagram "topic" [--style minimal|detailed|flowchart|network] [--save]'));
+    process.exit(1);
+    return;
+  }
+
+  const style = options.style || 'detailed';
+  const save = options.save || false;
+  const cost = STYLES[style]?.cost || 80;
+
+  console.log(chalk.hex('#F24E1E')('\n═══════════════════════════════════════════════════════════'));
+  console.log(chalk.white.bold('📊 ASCII DIAGRAM GENERATOR'));
+  console.log(chalk.hex('#F24E1E')('═══════════════════════════════════════════════════════════\n'));
+
+  console.log(chalk.white(`  📌 Topic: ${chalk.hex('#F24E1E')(topic)}`));
+  console.log(chalk.white(`  🎨 Style: ${chalk.hex('#F24E1E')(STYLES[style]?.name || 'Detailed')}`));
+  console.log(chalk.white(`  💰 Cost: ${chalk.green(cost + ' RCC')}`));
+
+  const spinner = new PremiumSpinner('Generating diagram');
+  spinner.start();
+
+  try {
+    const token = await getAuthToken();
+
+    spinner.update('Analyzing topic with AI');
+    await sleep(500);
+
+    // ✅ FIX: Use DEEP_RESEARCH task type (already supported by backend)
+    const response = await fetch(BACKEND_URL, {
+      method: 'POST',
+      headers: {
+        'Content-Type': 'application/json',
+        'Authorization': `Bearer ${token}`
+      },
+      body: JSON.stringify({
+        taskType: 'DEEP_RESEARCH',  // ← Use existing task type
+        message: `Generate a structured breakdown of "${topic}" for an ASCII diagram. 
+
+Return ONLY a valid JSON object with this exact structure (no other text):
+{
+  "components": ["component1", "component2", "component3", "component4"],
+  "methods": ["method1", "method2", "method3", "method4"],
+  "steps": ["step1", "step2", "step3", "step4", "step5"],
+  "nodes": ["node1", "node2", "node3"],
+  "outputs": ["output1", "output2", "output3"]
+}
+
+Make the components, methods, steps, nodes, and outputs specific to "${topic}".
+Return ONLY the JSON object, nothing else.`,
+        model: 'deep'
+      })
+    });
+
+    if (!response.ok) {
+      const errorText = await response.text();
+      throw new Error(`Backend returned ${response.status}: ${errorText.substring(0, 100)}`);
+    }
+
+    spinner.update('Rendering ASCII art');
+    await sleep(500);
+
+    const data = await response.json();
+    
+    // Parse AI response - extract JSON from the response
+    let aiData = {
+      components: [],
+      methods: [],
+      steps: [],
+      nodes: [],
+      outputs: []
+    };
+    
+    try {
+      // Try to find JSON in the response
+      const responseText = data.response || '';
+      const jsonMatch = responseText.match(/\{[\s\S]*\}/);
+      
+      if (jsonMatch) {
+        aiData = JSON.parse(jsonMatch[0]);
+      }
+    } catch (e) {
+      console.log(chalk.yellow('  ⚠ Using default structure'));
+    }
+
+    // Generate diagram based on style
+    let asciiDiagram;
+    switch (style) {
+      case 'minimal':
+        asciiDiagram = generateMinimalDiagram(topic, aiData);
+        break;
+      case 'flowchart':
+        asciiDiagram = generateFlowchartDiagram(topic, aiData);
+        break;
+      case 'network':
+        asciiDiagram = generateNetworkDiagram(topic, aiData);
+        break;
+      case 'detailed':
+      default:
+        asciiDiagram = generateDetailedDiagram(topic, aiData);
+        break;
+    }
+
+    spinner.succeed('✓ Diagram generated');
+
+    // Display diagram
+    console.log('\n' + chalk.cyan(asciiDiagram) + '\n');
+
+    // Save if requested
+    if (save) {
+      const timestamp = Date.now();
+      const safeTopic = topic.toLowerCase().replace(/[^a-z0-9]+/g, '-').substring(0, 50);
+      
+      // Save ASCII version
+      const txtFilename = `${safeTopic}-${timestamp}.txt`;
+      const txtPath = path.join(DIAGRAMS_DIR, txtFilename);
+      fs.writeFileSync(txtPath, asciiDiagram, 'utf8');
+      console.log(chalk.green(`  💾 Saved: ${txtPath}`));
+
+      // Save Markdown version
+      const mdFilename = `${safeTopic}-${timestamp}.md`;
+      const mdPath = path.join(DIAGRAMS_DIR, mdFilename);
+      const mdContent = `# ${topic} Research Diagram\n\n**Style:** ${STYLES[style].name}\n**Generated:** ${new Date().toLocaleString()}\n\n\`\`\`\n${asciiDiagram}\n\`\`\`\n`;
+      fs.writeFileSync(mdPath, mdContent, 'utf8');
+      console.log(chalk.green(`  💾 Saved: ${mdPath}`));
+    }
+
+    console.log(chalk.hex('#F24E1E')('\n═══════════════════════════════════════════════════════════\n'));
+
+  } catch (error) {
+    spinner.fail('Failed to generate diagram');
+    console.error(chalk.red(error.message));
+    
+    if (error.message.includes('402') || error.message.includes('Insufficient')) {
+      console.log(chalk.yellow('\n  💡 You need more RCC credits. Run: obx buy'));
+    }
+    
+    process.exit(1);
+  }
+}
+
+module.exports = { diagram, STYLES };