omnibiofex 4.1.0 → 4.3.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "omnibiofex",
-  "version": "4.1.0",
+  "version": "4.3.0",
   "description": "OmniBioFex X - The Autonomous Research Operating System",
   "main": "bin/obx",
   "bin": {

package/src/commands/diagram.js

@@ -13,186 +13,170 @@ if (!fs.existsSync(DIAGRAMS_DIR)) {
   fs.mkdirSync(DIAGRAMS_DIR, { recursive: true });
 }
 
-// Diagram styles
+// Diagram styles with costs
 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'
-  }
+  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 box
-function box(text, width = 60) {
-  const padding = Math.max(0, width - text.length - 2);
+// Generate ASCII banner (single line)
+function banner(title, width = 80) {
+  const safeTitle = (title || 'DIAGRAM').substring(0, width - 4);
+  const padding = width - safeTitle.length - 4;
   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}`;
+  return `╔${'═'.repeat(width)}╗\n║ ${' '.repeat(leftPad)}${safeTitle}${' '.repeat(rightPad)} ║\n╚${'═'.repeat(width)}╝`;
 }
 
-// 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);
+// Generate single-line node
+function nodeLine(text, width = 40) {
+  const safeText = (text || '').substring(0, width - 4);
+  const padding = width - safeText.length - 4;
   const leftPad = Math.floor(padding / 2);
   const rightPad = padding - leftPad;
-  const content = `│ ${' '.repeat(leftPad)}${text}${' '.repeat(rightPad)} │`;
-  return `${top}\n${content}\n${bottom}`;
+  return `┌${'─'.repeat(width)}┐\n│ ${' '.repeat(leftPad)}${safeText}${' '.repeat(rightPad)} │\n└${'─'.repeat(width)}┘`;
 }
 
 // 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▼';
-  }
+function arrow() {
+  return '│\n▼';
 }
 
-// Generate minimal diagram
-function generateMinimalDiagram(topic, components) {
+// Generate detailed diagram (vertical layout)
+function generateDetailedDiagram(topic, data) {
   const width = 60;
-  let diagram = banner(topic.toUpperCase(), width) + '\n\n';
+  let lines = [];
   
-  // Problem box
-  diagram += `${' '.repeat(20)}${node('Problem', 20)}\n`;
-  diagram += `${' '.repeat(29)}${arrow('down')}\n`;
+  lines.push(banner(`${topic.toUpperCase()} RESEARCH ECOSYSTEM`, width));
+  lines.push('');
   
-  // 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`;
+  // Problem
+  lines.push(nodeLine('Research Problem', width));
+  lines.push(arrow());
   
-  return diagram;
-}
-
-// Generate detailed diagram
-function generateDetailedDiagram(topic, components) {
-  const width = 80;
-  let diagram = banner(`${topic.toUpperCase()} RESEARCH ECOSYSTEM`, width) + '\n\n';
+  // Input sources (vertical list)
+  const sources = (data.components && data.components.length > 0) 
+    ? data.components.slice(0, 3) 
+    : ['Literature Review', 'Data Collection', 'Theory Analysis'];
   
-  // Problem identification
-  diagram += `${' '.repeat(25)}${node('Research Problem', 25)}\n`;
-  diagram += `${' '.repeat(37)}${arrow('down')}\n\n`;
+  lines.push(nodeLine('Input Sources', width));
+  lines.push(arrow());
+  sources.forEach(source => {
+    lines.push(`  • ${source}`);
+  });
+  lines.push(arrow());
   
-  // 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`;
+  // Integration
+  lines.push(nodeLine('Integration Layer', width));
+  lines.push(arrow());
   
   // Analysis phase
-  diagram += `${' '.repeat(20)}${node('Analysis Phase', 25)}\n`;
-  diagram += `${' '.repeat(32)}${arrow('down')}\n\n`;
+  lines.push(nodeLine('Analysis Phase', width));
+  lines.push(arrow());
   
-  // 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`;
+  const methods = (data.methods && data.methods.length > 0)
+    ? data.methods.slice(0, 4)
+    : ['Statistical Analysis', 'Qualitative Review', 'Comparative Study', 'Predictive Modeling'];
+  
+  lines.push(nodeLine('Methods', width));
+  lines.push(arrow());
+  methods.forEach(method => {
+    lines.push(`  • ${method}`);
+  });
+  lines.push(arrow());
+  
+  // Synthesis
+  lines.push(nodeLine('Synthesis & Insights', width));
+  lines.push(arrow());
   
   // Output phase
-  diagram += `${' '.repeat(20)}${node('Output Phase', 25)}\n`;
-  diagram += `${' '.repeat(32)}${arrow('down')}\n\n`;
+  lines.push(nodeLine('Output Phase', width));
+  lines.push(arrow());
+  
+  const outputs = (data.outputs && data.outputs.length > 0)
+    ? data.outputs.slice(0, 3)
+    : ['Publication', 'Implementation', 'Future Work'];
   
-  // Three outputs
-  diagram += `${node('Publication', 18)}     ${node('Implementation', 18)}     ${node('Future Work', 18)}\n`;
+  lines.push(nodeLine('Outputs', width));
+  lines.push(arrow());
+  outputs.forEach(output => {
+    lines.push(`  • ${output}`);
+  });
   
-  return diagram;
+  return lines.join('\n');
+}
+
+// Generate minimal diagram
+function generateMinimalDiagram(topic, data) {
+  const width = 50;
+  let lines = [];
+  
+  lines.push(banner(topic.toUpperCase(), width));
+  lines.push('');
+  lines.push(nodeLine('Problem', width));
+  lines.push(arrow());
+  lines.push(nodeLine('Research', width));
+  lines.push(arrow());
+  lines.push(nodeLine('Analysis', width));
+  lines.push(arrow());
+  lines.push(nodeLine('Solution', width));
+  
+  return lines.join('\n');
 }
 
 // Generate flowchart diagram
-function generateFlowchartDiagram(topic, steps) {
-  const width = 60;
-  let diagram = banner(`${topic.toUpperCase()} WORKFLOW`, width) + '\n\n';
+function generateFlowchartDiagram(topic, data) {
+  const width = 55;
+  const steps = (data.steps && data.steps.length > 0)
+    ? data.steps
+    : ['Research', 'Analysis', 'Implementation', 'Testing', 'Deployment'];
   
-  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)}${arrow('down')}\n`;
+  let lines = [];
+  lines.push(banner(`${topic.toUpperCase()} WORKFLOW`, width));
+  lines.push('');
+  
+  steps.forEach((step, i) => {
+    lines.push(nodeLine(`Step ${i + 1}: ${step}`, width));
+    if (i < steps.length - 1) {
+      lines.push(arrow());
     }
-    currentStep++;
-  }
+  });
   
-  diagram += `\n${' '.repeat(25)}${node('✓ Complete', 20)}\n`;
+  lines.push('');
+  lines.push(nodeLine('✓ Complete', width));
   
-  return diagram;
+  return lines.join('\n');
 }
 
 // Generate network diagram
-function generateNetworkDiagram(topic, nodes) {
-  const width = 70;
-  let diagram = banner(`${topic.toUpperCase()} NETWORK`, width) + '\n\n';
+function generateNetworkDiagram(topic, data) {
+  const width = 50;
+  const nodes = (data.nodes && data.nodes.length > 0)
+    ? data.nodes.slice(0, 5)
+    : ['Component A', 'Component B', 'Component C', 'Component D', 'Component E'];
+  
+  let lines = [];
+  lines.push(banner(`${topic.toUpperCase()} NETWORK`, width));
+  lines.push('');
   
   // 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`;
+  lines.push(nodeLine(topic, width));
+  lines.push(arrow());
   
-  // 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`;
+  // Connected nodes
+  lines.push(nodeLine('Connected Components', width));
+  lines.push(arrow());
+  nodes.forEach(node => {
+    lines.push(`  ├─ ${node}`);
+  });
+  lines.push(arrow());
   
-  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`;
+  // Integration
+  lines.push(nodeLine('Integration & Synthesis', width));
   
-  if (components && components.length > 0) {
-    components.forEach((comp, i) => {
-      mermaid += `    B --> E${i}[${comp}]\n`;
-    });
-  }
-  
-  mermaid += '```';
-  return mermaid;
+  return lines.join('\n');
 }
 
 // Main diagram command
@@ -205,14 +189,13 @@ async function diagram(topic, options = {}) {
 
   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]'));
+    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 publish = options.publish || false;
   const cost = STYLES[style]?.cost || 80;
 
   console.log(chalk.hex('#F24E1E')('\n═══════════════════════════════════════════════════════════'));
@@ -229,10 +212,10 @@ async function diagram(topic, options = {}) {
   try {
     const token = await getAuthToken();
 
-    // Call AI backend to get components/structure
     spinner.update('Analyzing topic with AI');
     await sleep(500);
 
+    // Use DEEP_RESEARCH task type (already supported by backend)
     const response = await fetch(BACKEND_URL, {
       method: 'POST',
       headers: {
@@ -240,22 +223,27 @@ async function diagram(topic, options = {}) {
         '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.`,
+        taskType: 'DEEP_RESEARCH',
+        message: `Generate a structured breakdown of "${topic}" for an ASCII diagram. 
+
+Return ONLY a valid JSON object with this exact structure (no other text):
+{
+  "components": ["component1", "component2", "component3"],
+  "methods": ["method1", "method2", "method3", "method4"],
+  "steps": ["step1", "step2", "step3", "step4", "step5"],
+  "nodes": ["node1", "node2", "node3", "node4", "node5"],
+  "outputs": ["output1", "output2", "output3"]
+}
+
+Make the components, methods, steps, nodes, and outputs specific to "${topic}".
+Return ONLY the JSON object, nothing else.`,
         model: 'deep'
       })
     });
 
     if (!response.ok) {
-      throw new Error(`Backend returned ${response.status}`);
+      const errorText = await response.text();
+      throw new Error(`Backend returned ${response.status}: ${errorText.substring(0, 100)}`);
     }
 
     spinner.update('Rendering ASCII art');
@@ -263,13 +251,26 @@ async function diagram(topic, options = {}) {
 
     const data = await response.json();
     
-    // Parse AI response
-    let aiData = { components: [], steps: [], nodes: [] };
+    // Parse AI response with safe defaults
+    let aiData = {
+      components: [],
+      methods: [],
+      steps: [],
+      nodes: [],
+      outputs: []
+    };
+    
     try {
-      // Try to extract JSON from response
-      const jsonMatch = data.response.match(/\{[\s\S]*\}/);
+      const responseText = data.response || '';
+      const jsonMatch = responseText.match(/\{[\s\S]*\}/);
+      
       if (jsonMatch) {
-        aiData = JSON.parse(jsonMatch[0]);
+        const parsed = JSON.parse(jsonMatch[0]);
+        aiData.components = Array.isArray(parsed.components) ? parsed.components : [];
+        aiData.methods = Array.isArray(parsed.methods) ? parsed.methods : [];
+        aiData.steps = Array.isArray(parsed.steps) ? parsed.steps : [];
+        aiData.nodes = Array.isArray(parsed.nodes) ? parsed.nodes : [];
+        aiData.outputs = Array.isArray(parsed.outputs) ? parsed.outputs : [];
       }
     } catch (e) {
       console.log(chalk.yellow('  ⚠ Using default structure'));
@@ -279,30 +280,27 @@ async function diagram(topic, options = {}) {
     let asciiDiagram;
     switch (style) {
       case 'minimal':
-        asciiDiagram = generateMinimalDiagram(topic, aiData.components);
+        asciiDiagram = generateMinimalDiagram(topic, aiData);
         break;
       case 'flowchart':
-        asciiDiagram = generateFlowchartDiagram(topic, aiData.steps.length > 0 ? aiData.steps : ['Research', 'Analysis', 'Implementation']);
+        asciiDiagram = generateFlowchartDiagram(topic, aiData);
         break;
       case 'network':
-        asciiDiagram = generateNetworkDiagram(topic, aiData.nodes);
+        asciiDiagram = generateNetworkDiagram(topic, aiData);
         break;
       case 'detailed':
       default:
-        asciiDiagram = generateDetailedDiagram(topic, aiData.components);
+        asciiDiagram = generateDetailedDiagram(topic, aiData);
         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) {
+    if (save) {
       const timestamp = Date.now();
       const safeTopic = topic.toLowerCase().replace(/[^a-z0-9]+/g, '-').substring(0, 50);
       
@@ -310,22 +308,14 @@ async function diagram(topic, options = {}) {
       const txtFilename = `${safeTopic}-${timestamp}.txt`;
       const txtPath = path.join(DIAGRAMS_DIR, txtFilename);
       fs.writeFileSync(txtPath, asciiDiagram, 'utf8');
-      console.log(chalk.green(`  💾 Saved ASCII: ${txtPath}`));
+      console.log(chalk.green(`  💾 Saved: ${txtPath}`));
 
-      // Save Markdown version with Mermaid
+      // 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:** ${new Date().toLocaleString()}\n\n## ASCII Diagram\n\n\`\`\`\n${asciiDiagram}\n\`\`\`\n\n## Mermaid Version\n\n${mermaidDiagram}\n`;
+      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 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.green(`  💾 Saved: ${mdPath}`));
     }
 
     console.log(chalk.hex('#F24E1E')('\n═══════════════════════════════════════════════════════════\n'));
@@ -333,6 +323,11 @@ async function diagram(topic, options = {}) {
   } 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);
   }
 }