omnibiofex 2.6.3 → 2.7.0

package/bin/obx

@@ -143,6 +143,29 @@ program
   .description('Open browser to purchase credits')
   .action(buy);
 
+// ==================== TIMELINE COMMAND ====================
+const { timeline } = require('../src/commands/timeline');
+
+program
+  .command('timeline')
+  .description('Generate research timeline for a topic')
+  .argument('<topic>', 'Research topic')
+  .action(timeline);
+
+// ==================== MORNING BRIEFING COMMAND ====================
+const { morning } = require('../src/commands/morning');
+
+program
+  .command('morning')
+  .description('Get your daily research briefing')
+  .action(morning);
+
+// Also add short alias
+program
+  .command('briefing')
+  .description('Get your daily research briefing (alias for morning)')
+  .action(morning);
+
 // ==================== DEBUG COMMAND ====================
 const { debug } = require('../src/commands/debug');
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "omnibiofex",
-  "version": "2.6.3",
+  "version": "2.7.0",
   "description": "OmniBioFex X - The Autonomous Research Terminal for AI-powered research missions",
   "main": "bin/obx",
   "bin": {

package/src/commands/morning.js

@@ -0,0 +1,94 @@
+const chalk = require('chalk');
+const { getAuthToken } = require('../auth');
+const { isAuthenticated } = require('../auth');
+const config = require('../config');
+const { 
+  displayMorningBriefing,
+  PremiumSpinner,
+  sleep 
+} = require('../utils/display');
+
+/**
+ * Fetch and display morning briefing
+ */
+async function morning() {
+  if (!isAuthenticated()) {
+    console.error(chalk.red('✗ Not authenticated. Please run: obx login'));
+    return;
+  }
+
+  const spinner = new PremiumSpinner('Fetching your research updates');
+  spinner.start();
+
+  try {
+    const token = await getAuthToken();
+    
+    spinner.update('Checking active missions');
+    await sleep(500);
+    
+    spinner.update('Scanning for new papers');
+    await sleep(500);
+    
+    spinner.update('Analyzing updates');
+    await sleep(500);
+    
+    // Call morning briefing API
+    const response = await fetch('https://morningbriefing-yyedhmslhq-uc.a.run.app', {
+      method: 'GET',
+      headers: {
+        'Authorization': `Bearer ${token}`,
+        'Content-Type': 'application/json'
+      }
+    });
+    
+    if (!response.ok) {
+      throw new Error(`API error: ${response.status}`);
+    }
+    
+    const briefing = await response.json();
+    
+    spinner.succeed('Briefing ready');
+    
+    // Display briefing
+    await displayMorningBriefing(briefing);
+    
+  } catch (error) {
+    spinner.fail('Failed to fetch morning briefing');
+    
+    // Fallback: show local briefing
+    console.log(chalk.gray('\n  Showing local briefing...\n'));
+    await displayLocalBriefing();
+  }
+}
+
+/**
+ * Display local briefing when API is unavailable
+ */
+async function displayLocalBriefing() {
+  const today = new Date().toLocaleDateString('en-US', { 
+    weekday: 'long', 
+    year: 'numeric', 
+    month: 'long', 
+    day: 'numeric' 
+  });
+  
+  const briefing = {
+    date: today,
+    updates: [
+      { type: 'info', text: 'No new updates since last check' },
+      { type: 'info', text: 'All missions are up to date' }
+    ],
+    missions: [
+      { name: 'Mission Atlas', status: 'Complete', progress: 100 }
+    ],
+    recommendations: [
+      'Run "obx morning" daily to stay updated',
+      'Check mission health with "obx mission status"',
+      'Explore new topics with "obx literature [topic]"'
+    ]
+  };
+  
+  await displayMorningBriefing(briefing);
+}
+
+module.exports = { morning };

package/src/commands/research.js

@@ -16,7 +16,9 @@ const {
   typeAIResponse,
   sleep,
   PremiumSpinner,
-  animateProgressBar
+  animateProgressBar,
+  calculateMissionHealth,      // Added
+  displayMissionHealth,        // Added
 } = require('../utils/display');
 
 const REPORTS_DIR = path.join(os.homedir(), 'obx-reports');
@@ -90,6 +92,19 @@ async function literatureReview(topic) {
     const score = generateResearchScore(result.response);
     await displayResearchScore(score);
     
+    // ===== NEW: Mission Health Score =====
+    const health = calculateMissionHealth({
+      evidenceScore: score.evidence,
+      noveltyScore: score.novelty,
+      confidenceScore: score.confidence,
+      methodologyScore: score.methodology,
+      reproducibilityScore: score.reproducibility,
+      citationsScore: score.citations,
+      gapsCount: Math.floor(Math.random() * 3) + 1
+    });
+    await displayMissionHealth(health, missionName);
+    // =====================================
+
     // Artifacts
     const artifacts = generateArtifacts('LITERATURE_REVIEW');
     await displayArtifacts(artifacts);

package/src/commands/timeline.js

@@ -0,0 +1,152 @@
+const chalk = require('chalk');
+const { createMission } = require('../api');
+const { isAuthenticated } = require('../auth');
+const { 
+  generateMissionName, 
+  displayTimeline,
+  PremiumSpinner,
+  sleep 
+} = require('../utils/display');
+
+/**
+ * Generate research timeline for a topic
+ */
+async function timeline(topic) {
+  if (!isAuthenticated()) {
+    console.error(chalk.red('✗ Not authenticated. Please run: obx login'));
+    return;
+  }
+
+  if (!topic || topic.trim() === '') {
+    console.error(chalk.red('✗ Please provide a research topic'));
+    console.log(chalk.gray('  Usage: obx timeline "quantum computing"'));
+    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(`Topic: ${topic}`));
+  console.log(chalk.gray(`Type: Research Timeline (80 RCC)\n`));
+
+  const spinner = new PremiumSpinner('Mapping research evolution');
+  spinner.start();
+
+  try {
+    spinner.update('Searching historical papers');
+    await sleep(800);
+    
+    spinner.update('Identifying key milestones');
+    await sleep(800);
+    
+    spinner.update('Building timeline graph');
+    await sleep(600);
+    
+    spinner.update('Analyzing impact');
+    await sleep(600);
+    
+    // Call backend API
+    const result = await createMission(
+      `Generate a comprehensive research timeline for: ${topic}. 
+      Include major papers, breakthroughs, patents, and milestones from the earliest research to present day.
+      Format as JSON array with objects containing: year, title, description, impact (High/Medium/Low), type (paper/patent/breakthrough/milestone).
+      Sort chronologically. Include 8-12 key events.`,
+      'RESEARCH_TIMELINE'
+    );
+    
+    spinner.succeed('Timeline generated');
+    
+    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`));
+
+    // Parse timeline from response
+    let timelineData = [];
+    
+    try {
+      // Try to extract JSON array from response
+      const jsonMatch = result.response.match(/\[[\s\S]*\]/);
+      if (jsonMatch) {
+        timelineData = JSON.parse(jsonMatch[0]);
+      }
+    } catch (e) {
+      // Fallback: generate sample timeline
+      timelineData = generateSampleTimeline(topic);
+    }
+    
+    // Add current research as final event
+    timelineData.push({
+      year: new Date().getFullYear(),
+      title: 'Your Research',
+      description: `Continuing the evolution of ${topic}`,
+      impact: 'High',
+      isCurrentResearch: true
+    });
+    
+    // Display timeline
+    await displayTimeline(timelineData, topic);
+    
+    console.log(chalk.green('✓ Timeline saved to: ') + chalk.white(`~/obx-reports/${missionName.replace(/\s+/g, '_')}_timeline.md`));
+    console.log(chalk.gray('\nView with: obx timeline "' + topic + '"\n'));
+    
+  } catch (error) {
+    spinner.fail('Failed to generate timeline');
+    console.error(chalk.red(error.response?.data?.error || error.message));
+  }
+}
+
+/**
+ * Generate sample timeline when API doesn't return structured data
+ */
+function generateSampleTimeline(topic) {
+  const currentYear = new Date().getFullYear();
+  
+  return [
+    {
+      year: currentYear - 30,
+      title: `Foundational Research on ${topic}`,
+      description: 'Early theoretical work and initial experiments',
+      impact: 'High',
+      type: 'paper'
+    },
+    {
+      year: currentYear - 20,
+      title: 'First Major Breakthrough',
+      description: 'Key discovery that shaped the field',
+      impact: 'High',
+      type: 'breakthrough'
+    },
+    {
+      year: currentYear - 15,
+      title: 'Commercial Applications Begin',
+      description: 'First industry implementations',
+      impact: 'Medium',
+      type: 'milestone'
+    },
+    {
+      year: currentYear - 10,
+      title: 'Patent Landscape Expands',
+      description: 'Significant patent filings by major companies',
+      impact: 'Medium',
+      type: 'patent'
+    },
+    {
+      year: currentYear - 5,
+      title: 'State-of-the-Art Advances',
+      description: 'Modern techniques and methodologies',
+      impact: 'High',
+      type: 'paper'
+    },
+    {
+      year: currentYear - 2,
+      title: 'Recent Breakthrough',
+      description: 'Latest major advancement in the field',
+      impact: 'High',
+      type: 'breakthrough'
+    }
+  ];
+}
+
+module.exports = { timeline };

package/src/utils/display.js

@@ -543,7 +543,7 @@ async function typeAIResponse(response) {
       continue;
     } else if (inTable) {
       // End of table
-      console.log(chalk.gray('└' + '─'.repeat(58) + '┘'));
+      console.log(chalk.gray('└' + '─'.repeat(58) + '┐'));
       console.log('');
       inTable = false;
       await sleep(100);
@@ -598,7 +598,7 @@ async function typeAIResponse(response) {
   
   // Close any open table
   if (inTable) {
-    console.log(chalk.gray('└' + '─'.repeat(58) + '┘'));
+    console.log(chalk.gray('└' + '─'.repeat(58) + '┐'));
   }
   
   console.log('\n' + chalk.gray('═'.repeat(60)) + '\n');
@@ -638,6 +638,239 @@ async function showThinking(taskType, topic) {
   }
 }
 
+// ==================== MISSION HEALTH SCORE ====================
+
+/**
+ * Calculate comprehensive mission health metrics
+ */
+function calculateMissionHealth(missionData) {
+  const evidence = missionData.evidenceScore || 96;
+  const novelty = missionData.noveltyScore || 81;
+  const confidence = missionData.confidenceScore || 91;
+  const methodology = missionData.methodologyScore || 89;
+  const reproducibility = missionData.reproducibilityScore || 93;
+  const citations = missionData.citationsScore || 98;
+  
+  // Calculate overall health (weighted average)
+  const overall = Math.round(
+    (evidence * 0.25) + 
+    (novelty * 0.15) + 
+    (confidence * 0.20) + 
+    (methodology * 0.15) + 
+    (reproducibility * 0.15) + 
+    (citations * 0.10)
+  );
+  
+  // Calculate bias risk
+  const biasRisk = overall >= 90 ? 'Low' : overall >= 75 ? 'Medium' : 'High';
+  
+  // Identify missing experiments based on gaps
+  const missingExperiments = missionData.gapsCount || Math.floor(Math.random() * 3) + 1;
+  
+  // Publication readiness
+  const publicationReady = overall >= 85 && evidence >= 90 && citations >= 95;
+  
+  return {
+    overall,
+    evidence,
+    novelty,
+    confidence,
+    methodology,
+    reproducibility,
+    citations,
+    biasRisk,
+    missingExperiments,
+    publicationReady
+  };
+}
+
+/**
+ * Display beautiful mission health score
+ */
+async function displayMissionHealth(health, missionName = 'Mission') {
+  console.log(chalk.hex('#F24E1E')('\n═══════════════════════════════════════════════════════════'));
+  console.log(chalk.white.bold(`🏥 ${missionName} - Health Score`));
+  console.log(chalk.hex('#F24E1E')('═══════════════════════════════════════════════════════════\n'));
+  
+  // Overall health with color coding
+  const overallColor = health.overall >= 90 ? chalk.green : 
+                       health.overall >= 75 ? chalk.yellow : chalk.red;
+  
+  console.log(chalk.gray('  Overall Health:'), overallColor.bold(`${health.overall}%`));
+  console.log('');
+  
+  // Detailed metrics
+  const metrics = [
+    { name: 'Evidence Strength', value: health.evidence },
+    { name: 'Novelty', value: health.novelty },
+    { name: 'Confidence', value: health.confidence },
+    { name: 'Methodological Quality', value: health.methodology },
+    { name: 'Reproducibility', value: health.reproducibility },
+    { name: 'Citation Completeness', value: health.citations }
+  ];
+  
+  for (const metric of metrics) {
+    const color = metric.value >= 90 ? chalk.green : 
+                  metric.value >= 75 ? chalk.yellow : chalk.red;
+    const bar = '█'.repeat(Math.floor(metric.value / 5)) + '░'.repeat(20 - Math.floor(metric.value / 5));
+    
+    process.stdout.write(chalk.gray(`  ${metric.name.padEnd(25)} `));
+    await typeText(`${metric.value}%`, 20, color);
+    process.stdout.write(` ${chalk.gray(bar)}\n`);
+    await sleep(80);
+  }
+  
+  console.log('');
+  
+  // Risk assessment
+  const biasColor = health.biasRisk === 'Low' ? chalk.green : 
+                    health.biasRisk === 'Medium' ? chalk.yellow : chalk.red;
+  console.log(chalk.gray('  Bias Risk:'), biasColor.bold(health.biasRisk));
+  
+  // Missing experiments
+  if (health.missingExperiments > 0) {
+    console.log(
+      chalk.gray('  Missing Experiments:'),
+      chalk.yellow.bold(`${health.missingExperiments}`)
+    );
+  } else {
+    console.log(chalk.gray('  Missing Experiments:'), chalk.green.bold('None ✓'));
+  }
+  
+  // Publication readiness
+  console.log(
+    chalk.gray('  Publication Ready:'),
+    health.publicationReady ? chalk.green.bold('Yes ✓') : chalk.yellow.bold('Needs Review')
+  );
+  
+  console.log(chalk.hex('#F24E1E')('\n═══════════════════════════════════════════════════════════\n'));
+}
+
+// ==================== RESEARCH TIMELINE VISUALIZATION ====================
+
+/**
+ * Display beautiful research timeline
+ */
+async function displayTimeline(timeline, topic) {
+  console.log(chalk.hex('#F24E1E')('\n═══════════════════════════════════════════════════════════'));
+  console.log(chalk.white.bold(`📅 Research Timeline: ${topic}`));
+  console.log(chalk.hex('#F24E1E')('═══════════════════════════════════════════════════════════\n'));
+  
+  if (!timeline || timeline.length === 0) {
+    console.log(chalk.gray('  No timeline data available.\n'));
+    return;
+  }
+  
+  // Sort by year
+  const sorted = [...timeline].sort((a, b) => a.year - b.year);
+  
+  for (let i = 0; i < sorted.length; i++) {
+    const event = sorted[i];
+    const isLast = i === sorted.length - 1;
+    const isCurrent = event.isCurrentResearch;
+    
+    // Year
+    process.stdout.write(chalk.hex('#F24E1E').bold(`  ${event.year} `));
+    
+    // Connector line
+    if (!isLast) {
+      process.stdout.write(chalk.gray('──── '));
+    } else {
+      process.stdout.write(chalk.gray('──── '));
+    }
+    
+    // Event title
+    if (isCurrent) {
+      await typeText(event.title, 10, chalk.green.bold);
+    } else {
+      await typeText(event.title, 10, chalk.white);
+    }
+    
+    console.log('');
+    
+    // Description
+    if (event.description) {
+      console.log(chalk.gray(`         ${event.description}`));
+    }
+    
+    // Impact
+    if (event.impact) {
+      const impactColor = event.impact === 'High' ? chalk.red : 
+                          event.impact === 'Medium' ? chalk.yellow : chalk.gray;
+      console.log(chalk.gray(`         Impact: `), impactColor(event.impact));
+    }
+    
+    // Vertical connector
+    if (!isLast) {
+      console.log(chalk.gray('         │'));
+    } else {
+      console.log('');
+      console.log(chalk.green.bold('         ✨ Your research continues from here'));
+    }
+    
+    console.log('');
+    await sleep(150);
+  }
+  
+  console.log(chalk.hex('#F24E1E')('═══════════════════════════════════════════════════════════\n'));
+}
+
+// ==================== MORNING BRIEFING DISPLAY ====================
+
+/**
+ * Display morning briefing
+ */
+async function displayMorningBriefing(briefing) {
+  console.log(chalk.hex('#F24E1E')('\n═══════════════════════════════════════════════════════════'));
+  console.log(chalk.white.bold('☀️  Good Morning, Researcher!'));
+  console.log(chalk.hex('#F24E1E')('═══════════════════════════════════════════════════════════\n'));
+  
+  console.log(chalk.gray(`  ${briefing.date}\n`));
+  
+  if (briefing.updates && briefing.updates.length > 0) {
+    console.log(chalk.white.bold('  📊 Mission Updates:\n'));
+    
+    for (const update of briefing.updates) {
+      const icon = update.type === 'paper' ? '📄' : 
+                   update.type === 'patent' ? '📜' : 
+                   update.type === 'citation' ? '🔗' : 
+                   update.type === 'contradiction' ? '⚠️' : '📌';
+      
+      process.stdout.write(chalk.gray(`    ${icon} `));
+      await typeText(update.text, 8, chalk.white);
+      console.log('');
+      await sleep(100);
+    }
+  }
+  
+  if (briefing.missions && briefing.missions.length > 0) {
+    console.log(chalk.white.bold('\n  🎯 Active Missions:\n'));
+    
+    for (const mission of briefing.missions) {
+      const statusColor = mission.status === 'Running' ? chalk.yellow : 
+                          mission.status === 'Complete' ? chalk.green : chalk.gray;
+      
+      console.log(chalk.gray(`    ✨ ${mission.name}`));
+      console.log(statusColor(`       Status: ${mission.status}`));
+      console.log(chalk.gray(`       Progress: ${mission.progress}%`));
+      console.log('');
+    }
+  }
+  
+  if (briefing.recommendations && briefing.recommendations.length > 0) {
+    console.log(chalk.white.bold('  💡 Recommendations:\n'));
+    
+    for (const rec of briefing.recommendations) {
+      process.stdout.write(chalk.gray('    ▸ '));
+      await typeText(rec, 8, chalk.white);
+      console.log('');
+      await sleep(80);
+    }
+  }
+  
+  console.log(chalk.hex('#F24E1E')('\n═══════════════════════════════════════════════════════════\n'));
+}
+
 module.exports = {
   generateMissionName,
   sleep,
@@ -660,4 +893,9 @@ module.exports = {
   showThinking,
   formatTable,
   addVisualBreak,
+  // NEW EXPORTS
+  calculateMissionHealth,
+  displayMissionHealth,
+  displayTimeline,
+  displayMorningBriefing,
 };