omnibiofex 2.7.0 → 2.7.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "omnibiofex",
-  "version": "2.7.0",
+  "version": "2.7.1",
   "description": "OmniBioFex X - The Autonomous Research Terminal for AI-powered research missions",
   "main": "bin/obx",
   "bin": {

package/src/commands/data.js

@@ -1,58 +1,269 @@
 const chalk = require('chalk');
-const ora = require('ora');
+const fs = require('fs');
+const path = require('path');
+const os = require('os');
+const { createMission } = require('../api');
 const { isAuthenticated } = require('../auth');
+const {
+  generateMissionName,
+  displayMissionDashboard,
+  displayResearchScore,
+  displayArtifacts,
+  generateResearchScore,
+  generateArtifacts,
+  typeAIResponse,
+  PremiumSpinner,
+  sleep,
+  animateResearchSources
+} = require('../utils/display');
 
+const REPORTS_DIR = path.join(os.homedir(), 'obx-reports');
+if (!fs.existsSync(REPORTS_DIR)) {
+  fs.mkdirSync(REPORTS_DIR, { recursive: true });
+}
+
+function saveReport(topic, content, missionName) {
+  const timestamp = new Date().toISOString().replace(/[:.]/g, '-');
+  const sanitizedTopic = topic.replace(/[^a-z0-9]/gi, '_').substring(0, 50);
+  const filename = `${missionName.replace(/\s+/g, '_')}_${timestamp}.md`;
+  const filepath = path.join(REPORTS_DIR, filename);
+  
+  fs.writeFileSync(filepath, content, 'utf8');
+  return filepath;
+}
+
+// ==================== DATASET ANALYSIS ====================
 async function dataset(file) {
   if (!isAuthenticated()) {
-    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    console.error(chalk.red('✗ Not authenticated. Please run: obx login'));
+    return;
+  }
+
+  if (!fs.existsSync(file)) {
+    console.error(chalk.red(`✗ File not found: ${file}`));
     return;
   }
 
-  const spinner = ora(`Analyzing dataset: ${file}`).start();
+  const missionName = generateMissionName();
+  
+  console.log(chalk.hex('#F24E1E')('\n═══════════════════════════════════════════════════════════'));
+  console.log(chalk.white.bold(`✨ ${missionName}`));
+  console.log(chalk.hex('#F24E1E')('═══════════════════════════════════════════════════════════'));
+  console.log(chalk.gray(`File: ${file}`));
+  console.log(chalk.gray(`Type: Dataset Analysis (40-150 RCC)\n`));
+
+  const spinner = new PremiumSpinner('Reading dataset');
+  spinner.start();
 
   try {
-    spinner.succeed(chalk.green('Dataset analysis complete!'));
-    console.log(chalk.gray('\n✓ Analysis generated successfully.\n'));
+    spinner.update('Parsing data structure');
+    await sleep(600);
+    
+    spinner.update('Detecting patterns');
+    await sleep(600);
+    
+    spinner.update('Calculating statistics');
+    await sleep(600);
+    
+    // Read file content (first 5000 chars for large files)
+    const fileContent = fs.readFileSync(file, 'utf8').substring(0, 5000);
+    
+    const result = await createMission(
+      `Analyze this dataset and provide:\n1. Statistical summary (mean, median, std dev, min, max)\n2. Pattern detection\n3. Anomaly identification\n4. Data quality assessment\n5. Visualization recommendations\n\nDataset content:\n${fileContent}`,
+      'DATASET_ANALYSIS'
+    );
+    
+    spinner.succeed('Dataset analysis complete');
+    
+    console.log(chalk.gray(`\n📊 Model: ${result.model}`));
+    console.log(chalk.gray(`💰 RCC Cost: ${result.rccCost}`));
+    console.log(chalk.gray(`💳 Remaining Balance: ${result.rccBalance} RCC\n`));
+
+    // Display the analysis with typing animation
+    await typeAIResponse(result.response);
+    
+    // Research score
+    const score = generateResearchScore(result.response);
+    await displayResearchScore(score);
+    
+    // Artifacts
+    const artifacts = [
+      { icon: '📊', name: 'Statistical Summary' },
+      { icon: '🔍', name: 'Pattern Report' },
+      { icon: '⚠️', name: 'Anomaly Detection' },
+      { icon: '📈', name: 'Data Quality Assessment' }
+    ];
+    await displayArtifacts(artifacts);
+    
+    // Save report
+    const filepath = saveReport(file, result.response, missionName);
+    console.log(chalk.green(`✓ Report saved to: ${filepath}`));
+    console.log(chalk.gray('\nView with: cat ' + filepath + '\n'));
     
   } catch (error) {
-    spinner.fail(chalk.red('Failed to analyze dataset'));
-    console.error(chalk.red(error.message));
+    spinner.fail('Failed to analyze dataset');
+    console.error(chalk.red(error.response?.data?.error || error.message));
   }
 }
 
-async function code(directory) {
+// ==================== CODE REVIEW ====================
+async function code(directory = '.') {
   if (!isAuthenticated()) {
-    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    console.error(chalk.red('✗ Not authenticated. Please run: obx login'));
     return;
   }
 
-  const spinner = ora(`Reviewing code in: ${directory}`).start();
+  if (!fs.existsSync(directory)) {
+    console.error(chalk.red(`✗ Directory not found: ${directory}`));
+    return;
+  }
+
+  const missionName = generateMissionName();
+  
+  console.log(chalk.hex('#F24E1E')('\n═══════════════════════════════════════════════════════════'));
+  console.log(chalk.white.bold(`✨ ${missionName}`));
+  console.log(chalk.hex('#F24E1E')('═══════════════════════════════════════════════════════════'));
+  console.log(chalk.gray(`Directory: ${directory}`));
+  console.log(chalk.gray(`Type: Code Review (40-300 RCC)\n`));
+
+  const spinner = new PremiumSpinner('Scanning repository');
+  spinner.start();
 
   try {
-    spinner.succeed(chalk.green('Code review complete!'));
-    console.log(chalk.gray('\n✓ Review generated successfully.\n'));
+    spinner.update('Analyzing architecture');
+    await sleep(800);
+    
+    spinner.update('Security audit');
+    await sleep(800);
+    
+    spinner.update('Performance review');
+    await sleep(600);
+    
+    // Read key files from directory
+    const files = fs.readdirSync(directory).filter(f => 
+      f.endsWith('.js') || f.endsWith('.py') || f.endsWith('.ts') || 
+      f.endsWith('.java') || f.endsWith('.cpp') || f.endsWith('.go')
+    ).slice(0, 10); // Limit to 10 files
+    
+    let codeContent = '';
+    for (const file of files) {
+      const filePath = path.join(directory, file);
+      if (fs.statSync(filePath).isFile()) {
+        codeContent += `\n\n// File: ${file}\n`;
+        codeContent += fs.readFileSync(filePath, 'utf8').substring(0, 2000);
+      }
+    }
+    
+    const result = await createMission(
+      `Review this code repository and provide:\n1. Architecture analysis\n2. Security vulnerabilities\n3. Performance issues\n4. Code quality assessment\n5. Optimization suggestions\n6. Best practices recommendations\n\nCode:\n${codeContent}`,
+      'CODE_REVIEW'
+    );
+    
+    spinner.succeed('Code review complete');
+    
+    console.log(chalk.gray(`\n📊 Model: ${result.model}`));
+    console.log(chalk.gray(`💰 RCC Cost: ${result.rccCost}`));
+    console.log(chalk.gray(`💳 Remaining Balance: ${result.rccBalance} RCC\n`));
+
+    // Display the review with typing animation
+    await typeAIResponse(result.response);
+    
+    // Research score
+    const score = generateResearchScore(result.response);
+    await displayResearchScore(score);
+    
+    // Artifacts
+    const artifacts = [
+      { icon: '🏗️', name: 'Architecture Report' },
+      { icon: '🔐', name: 'Security Audit' },
+      { icon: '⚡', name: 'Performance Analysis' },
+      { icon: '💡', name: 'Optimization Suggestions' }
+    ];
+    await displayArtifacts(artifacts);
+    
+    // Save report
+    const filepath = saveReport(directory, result.response, missionName);
+    console.log(chalk.green(`✓ Report saved to: ${filepath}`));
+    console.log(chalk.gray('\nView with: cat ' + filepath + '\n'));
     
   } catch (error) {
-    spinner.fail(chalk.red('Failed to review code'));
-    console.error(chalk.red(error.message));
+    spinner.fail('Failed to review code');
+    console.error(chalk.red(error.response?.data?.error || error.message));
   }
 }
 
+// ==================== MEDICAL IMAGING ANALYSIS ====================
 async function medical(file) {
   if (!isAuthenticated()) {
-    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    console.error(chalk.red('✗ Not authenticated. Please run: obx login'));
+    return;
+  }
+
+  if (!fs.existsSync(file)) {
+    console.error(chalk.red(`✗ File not found: ${file}`));
     return;
   }
 
-  const spinner = ora(`Analyzing medical imaging: ${file}`).start();
+  const missionName = generateMissionName();
+  
+  console.log(chalk.hex('#F24E1E')('\n═══════════════════════════════════════════════════════════'));
+  console.log(chalk.white.bold(`✨ ${missionName}`));
+  console.log(chalk.hex('#F24E1E')('═══════════════════════════════════════════════════════════'));
+  console.log(chalk.gray(`File: ${file}`));
+  console.log(chalk.gray(`Type: Medical Imaging Analysis (30-120 RCC)\n`));
+
+  const spinner = new PremiumSpinner('Loading medical image');
+  spinner.start();
 
   try {
-    spinner.succeed(chalk.green('Medical analysis complete!'));
-    console.log(chalk.gray('\n✓ Analysis generated successfully.\n'));
+    spinner.update('Analyzing image patterns');
+    await sleep(800);
+    
+    spinner.update('Detecting anomalies');
+    await sleep(800);
+    
+    spinner.update('Comparing with reference database');
+    await sleep(600);
+    
+    // For images, we send metadata and ask for analysis
+    const stats = fs.statSync(file);
+    const fileExt = path.extname(file).toLowerCase();
+    
+    const result = await createMission(
+      `Analyze this medical imaging file and provide a comprehensive research-oriented analysis:\n\nFile: ${path.basename(file)}\nFormat: ${fileExt}\nSize: ${stats.size} bytes\n\nPlease provide:\n1. Image type identification (X-ray, MRI, CT, Ultrasound, etc.)\n2. Anatomical region identification\n3. Pattern detection and findings\n4. Potential anomalies or areas of interest\n5. Comparative analysis with typical presentations\n6. Research implications and suggested further investigation\n7. Confidence level and limitations\n\nNote: This is for research purposes only, not clinical diagnosis.`,
+      'MEDICAL_ANALYSIS'
+    );
+    
+    spinner.succeed('Medical analysis complete');
+    
+    console.log(chalk.gray(`\n📊 Model: ${result.model}`));
+    console.log(chalk.gray(`💰 RCC Cost: ${result.rccCost}`));
+    console.log(chalk.gray(`💳 Remaining Balance: ${result.rccBalance} RCC\n`));
+
+    // 🔥 THIS WAS MISSING - Display the analysis with typing animation
+    await typeAIResponse(result.response);
+    
+    // Research score
+    const score = generateResearchScore(result.response);
+    await displayResearchScore(score);
+    
+    // Artifacts
+    const artifacts = [
+      { icon: '🏥', name: 'Pattern Detection Report' },
+      { icon: '🔍', name: 'Anomaly Analysis' },
+      { icon: '📊', name: 'Comparative Analysis' },
+      { icon: '📝', name: 'Research Implications' }
+    ];
+    await displayArtifacts(artifacts);
+    
+    // Save report
+    const filepath = saveReport(file, result.response, missionName);
+    console.log(chalk.green(`✓ Report saved to: ${filepath}`));
+    console.log(chalk.gray('\nView with: cat ' + filepath + '\n'));
     
   } catch (error) {
-    spinner.fail(chalk.red('Failed to analyze medical imaging'));
-    console.error(chalk.red(error.message));
+    spinner.fail('Failed to analyze medical image');
+    console.error(chalk.red(error.response?.data?.error || error.message));
   }
 }
 

package/src/commands/research.js

@@ -17,8 +17,8 @@ const {
   sleep,
   PremiumSpinner,
   animateProgressBar,
-  calculateMissionHealth,      // Added
-  displayMissionHealth,        // Added
+  calculateMissionHealth,
+  displayMissionHealth,
 } = require('../utils/display');
 
 const REPORTS_DIR = path.join(os.homedir(), 'obx-reports');
@@ -154,12 +154,29 @@ async function paper(file) {
     
     console.log(chalk.gray(`\n📊 Model: ${result.model}`));
     console.log(chalk.gray(`💰 RCC Cost: ${result.rccCost}`));
-    
+    console.log(chalk.gray(`💳 Remaining Balance: ${result.rccBalance} RCC\n`));
+
+    // 🔥 Display the analysis
     await typeAIResponse(result.response);
-    
+
+    // Research score
     const score = generateResearchScore(result.response);
     await displayResearchScore(score);
-    
+
+    // Artifacts
+    const artifacts = [
+      { icon: '📄', name: 'Paper Analysis' },
+      { icon: '🔍', name: 'Key Claims' },
+      { icon: '📊', name: 'Methodology Evaluation' },
+      { icon: '⚠️', name: 'Limitations' }
+    ];
+    await displayArtifacts(artifacts);
+
+    // Save report
+    const filepath = saveReport(file, result.response, missionName);
+    console.log(chalk.green(`✓ Report saved to: ${filepath}`));
+    console.log(chalk.gray('\nView with: cat ' + filepath + '\n'));
+
   } catch (error) {
     spinner.fail('Failed to analyze paper');
     console.error(chalk.red(error.response?.data?.error || error.message));
@@ -203,9 +220,29 @@ async function compare(files) {
     
     console.log(chalk.gray(`\n📊 Model: ${result.model}`));
     console.log(chalk.gray(`💰 RCC Cost: ${result.rccCost}`));
-    
+    console.log(chalk.gray(`💳 Remaining Balance: ${result.rccBalance} RCC\n`));
+
+    // 🔥 Display the comparison
     await typeAIResponse(result.response);
-    
+
+    // Research score
+    const score = generateResearchScore(result.response);
+    await displayResearchScore(score);
+
+    // Artifacts
+    const artifacts = [
+      { icon: '📊', name: 'Comparison Matrix' },
+      { icon: '⚠️', name: 'Contradiction Report' },
+      { icon: '🔍', name: 'Methodology Comparison' },
+      { icon: '✍️', name: 'Synthesis Report' }
+    ];
+    await displayArtifacts(artifacts);
+
+    // Save report
+    const filepath = saveReport(files.join('_'), result.response, missionName);
+    console.log(chalk.green(`✓ Report saved to: ${filepath}`));
+    console.log(chalk.gray('\nView with: cat ' + filepath + '\n'));
+
   } catch (error) {
     spinner.fail('Failed to compare papers');
     console.error(chalk.red(error.response?.data?.error || error.message));