omnibiofex 4.0.0 → 4.1.0

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": "4.1.0",
   "description": "OmniBioFex X - The Autonomous Research Operating System",
   "main": "bin/obx",
   "bin": {

package/src/commands/diagram.js

@@ -0,0 +1,340 @@
+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
+const STYLES = {
+  minimal: {
+    name: 'Minimal',
+    cost: 40,
+    description: 'Clean, simple flowchart'
+  },
+  detailed: {
+    name: 'Detailed',
+    cost: 80,
+    description: 'Comprehensive ecosystem with all components'
+  },
+  flowchart: {
+    name: 'Flowchart',
+    cost: 60,
+    description: 'Step-by-step process flow'
+  },
+  network: {
+    name: 'Network',
+    cost: 70,
+    description: 'Interconnected nodes and relationships'
+  }
+};
+
+// Generate ASCII box
+function box(text, width = 60) {
+  const padding = Math.max(0, width - text.length - 2);
+  const leftPad = Math.floor(padding / 2);
+  const rightPad = padding - leftPad;
+  return `║ ${' '.repeat(leftPad)}${text}${' '.repeat(rightPad)} ║`;
+}
+
+// Generate ASCII banner
+function banner(title, width = 80) {
+  const top = `╔${'═'.repeat(width)}╗`;
+  const bottom = `╚${'═'.repeat(width)}╝`;
+  const content = box(title, width);
+  return `${top}\n${content}\n${bottom}`;
+}
+
+// Generate node box
+function node(text, width = 20) {
+  const top = `┌${'─'.repeat(width)}┐`;
+  const bottom = `└${'─'.repeat(width)}┘`;
+  const padding = Math.max(0, width - text.length - 2);
+  const leftPad = Math.floor(padding / 2);
+  const rightPad = padding - leftPad;
+  const content = `│ ${' '.repeat(leftPad)}${text}${' '.repeat(rightPad)} │`;
+  return `${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 minimal diagram
+function generateMinimalDiagram(topic, components) {
+  const width = 60;
+  let diagram = banner(topic.toUpperCase(), width) + '\n\n';
+  
+  // Problem box
+  diagram += `${' '.repeat(20)}${node('Problem', 20)}\n`;
+  diagram += `${' '.repeat(29)}${arrow('down')}\n`;
+  
+  // Three branches
+  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 detailed diagram
+function generateDetailedDiagram(topic, components) {
+  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)}${arrow('down')}\n\n`;
+  
+  // Three input sources
+  diagram += `${' '.repeat(5)}${node('Literature', 18)}     ${node('Data', 18)}     ${node('Theory', 18)}\n`;
+  diagram += `${' '.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)}${arrow('down')}\n\n`;
+  
+  // Four analysis types
+  diagram += `${node('Statistical', 14)}  ${node('Qualitative', 14)}  ${node('Comparative', 14)}  ${node('Predictive', 14)}\n`;
+  diagram += `${' '.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)}${arrow('down')}\n\n`;
+  
+  // Three outputs
+  diagram += `${node('Publication', 18)}     ${node('Implementation', 18)}     ${node('Future Work', 18)}\n`;
+  
+  return diagram;
+}
+
+// Generate flowchart diagram
+function generateFlowchartDiagram(topic, steps) {
+  const width = 60;
+  let diagram = banner(`${topic.toUpperCase()} WORKFLOW`, width) + '\n\n';
+  
+  let currentStep = 1;
+  for (const step of steps) {
+    const stepText = `Step ${currentStep}: ${step}`;
+    diagram += `${' '.repeat(15)}${node(stepText, 45)}\n`;
+    if (currentStep < steps.length) {
+      diagram += `${' '.repeat(37)}${arrow('down')}\n`;
+    }
+    currentStep++;
+  }
+  
+  diagram += `\n${' '.repeat(25)}${node('✓ Complete', 20)}\n`;
+  
+  return diagram;
+}
+
+// Generate network diagram
+function generateNetworkDiagram(topic, nodes) {
+  const width = 70;
+  let diagram = banner(`${topic.toUpperCase()} NETWORK`, width) + '\n\n';
+  
+  // Central node
+  diagram += `${' '.repeat(25)}${node(topic, 25)}\n`;
+  diagram += `${' '.repeat(37)}|\n`;
+  diagram += `${' '.repeat(20)}┌────────┼────────┐\n`;
+  diagram += `${' '.repeat(20)}│        │        │\n`;
+  diagram += `${' '.repeat(20)}▼        ▼        ▼\n`;
+  
+  // Three connected nodes
+  diagram += `${node(nodes[0] || 'Node A', 18)}  ${node(nodes[1] || 'Node B', 18)}  ${node(nodes[2] || 'Node C', 18)}\n`;
+  diagram += `${' '.repeat(9)}│        │        │\n`;
+  diagram += `${' '.repeat(9)}└────────┼────────┘\n`;
+  diagram += `${' '.repeat(18)}▼\n`;
+  diagram += `${' '.repeat(15)}${node('Integration', 25)}\n`;
+  
+  return diagram;
+}
+
+// Generate Mermaid diagram for markdown
+function generateMermaidDiagram(topic, components, style) {
+  let mermaid = '```mermaid\n';
+  mermaid += 'graph TD\n';
+  mermaid += `    A[${topic}] --> B[Research Phase]\n`;
+  mermaid += `    B --> C[Analysis Phase]\n`;
+  mermaid += `    C --> D[Output Phase]\n`;
+  
+  if (components && components.length > 0) {
+    components.forEach((comp, i) => {
+      mermaid += `    B --> E${i}[${comp}]\n`;
+    });
+  }
+  
+  mermaid += '```';
+  return mermaid;
+}
+
+// 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] [--publish]'));
+    process.exit(1);
+    return;
+  }
+
+  const style = options.style || 'detailed';
+  const save = options.save || false;
+  const publish = options.publish || 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();
+
+    // Call AI backend to get components/structure
+    spinner.update('Analyzing topic with AI');
+    await sleep(500);
+
+    const response = await fetch(BACKEND_URL, {
+      method: 'POST',
+      headers: {
+        'Content-Type': 'application/json',
+        'Authorization': `Bearer ${token}`
+      },
+      body: JSON.stringify({
+        taskType: 'RESEARCH_DIAGRAM',
+        message: `Generate a structured breakdown of "${topic}" for an ASCII diagram. Return a JSON object with:
+        {
+          "components": ["component1", "component2", ...],
+          "steps": ["step1", "step2", ...],
+          "nodes": ["node1", "node2", "node3"],
+          "description": "brief description"
+        }
+        
+        Only return valid JSON, no other text.`,
+        model: 'deep'
+      })
+    });
+
+    if (!response.ok) {
+      throw new Error(`Backend returned ${response.status}`);
+    }
+
+    spinner.update('Rendering ASCII art');
+    await sleep(500);
+
+    const data = await response.json();
+    
+    // Parse AI response
+    let aiData = { components: [], steps: [], nodes: [] };
+    try {
+      // Try to extract JSON from response
+      const jsonMatch = data.response.match(/\{[\s\S]*\}/);
+      if (jsonMatch) {
+        aiData = JSON.parse(jsonMatch[0]);
+      }
+    } catch (e) {
+      console.log(chalk.yellow('  ⚠ Using default structure'));
+    }
+
+    // Generate diagram based on style
+    let asciiDiagram;
+    switch (style) {
+      case 'minimal':
+        asciiDiagram = generateMinimalDiagram(topic, aiData.components);
+        break;
+      case 'flowchart':
+        asciiDiagram = generateFlowchartDiagram(topic, aiData.steps.length > 0 ? aiData.steps : ['Research', 'Analysis', 'Implementation']);
+        break;
+      case 'network':
+        asciiDiagram = generateNetworkDiagram(topic, aiData.nodes);
+        break;
+      case 'detailed':
+      default:
+        asciiDiagram = generateDetailedDiagram(topic, aiData.components);
+        break;
+    }
+
+    // Generate Mermaid version
+    const mermaidDiagram = generateMermaidDiagram(topic, aiData.components, style);
+
+    spinner.succeed('✓ Diagram generated');
+
+    // Display diagram
+    console.log('\n' + chalk.cyan(asciiDiagram) + '\n');
+
+    // Save if requested
+    if (save || publish) {
+      const timestamp = Date.now();
+      const safeTopic = topic.toLowerCase().replace(/[^a-z0-9]+/g, '-').substring(0, 50);
+      
+      // Save ASCII version
+      const txtFilename = `${safeTopic}-${timestamp}.txt`;
+      const txtPath = path.join(DIAGRAMS_DIR, txtFilename);
+      fs.writeFileSync(txtPath, asciiDiagram, 'utf8');
+      console.log(chalk.green(`  💾 Saved ASCII: ${txtPath}`));
+
+      // Save Markdown version with Mermaid
+      const mdFilename = `${safeTopic}-${timestamp}.md`;
+      const mdPath = path.join(DIAGRAMS_DIR, mdFilename);
+      const mdContent = `# ${topic} Research Diagram\n\n**Style:** ${STYLES[style].name}\n**Generated:** ${new Date().toLocaleString()}\n\n## ASCII Diagram\n\n\`\`\`\n${asciiDiagram}\n\`\`\`\n\n## Mermaid Version\n\n${mermaidDiagram}\n`;
+      fs.writeFileSync(mdPath, mdContent, 'utf8');
+      console.log(chalk.green(`  💾 Saved Markdown: ${mdPath}`));
+    }
+
+    // Publish if requested
+    if (publish) {
+      console.log(chalk.yellow('\n  📤 To publish this diagram as research:'));
+      console.log(chalk.gray('  1. Review the saved markdown file'));
+      console.log(chalk.gray('  2. Run: obx publish'));
+      console.log(chalk.gray('  3. Select the diagram from your missions'));
+    }
+
+    console.log(chalk.hex('#F24E1E')('\n═══════════════════════════════════════════════════════════\n'));
+
+  } catch (error) {
+    spinner.fail('Failed to generate diagram');
+    console.error(chalk.red(error.message));
+    process.exit(1);
+  }
+}
+
+module.exports = { diagram, STYLES };