omnibiofex 2.5.0 → 2.6.0

package/bin/obx

@@ -1,46 +1,160 @@
 #!/usr/bin/env node
+
 const { program } = require('commander');
 const chalk = require('chalk');
 const figlet = require('figlet');
-const { login, logout } = require('../src/auth');
-const { missionCreate, missionStatus, missionResults, missionList } = require('../src/commands/mission');
-const { literatureReview, gaps, hypothesis } = require('../src/commands/research');
-const { credits, usage, buy } = require('../src/commands/account');
-const { debug } = require('../src/commands/debug');
+const path = require('path');
+const fs = require('fs');
+
+// 🔥 FIX: Read version dynamically from package.json
+const packageJson = JSON.parse(
+  fs.readFileSync(path.join(__dirname, '../package.json'), 'utf8')
+);
+const VERSION = packageJson.version;
 
+// Display banner
+console.log(
+  chalk.hex('#F24E1E')(
+    figlet.textSync('OmniBioFex X', { horizontalLayout: 'full' })
+  )
+);
+console.log(chalk.gray(`The Autonomous Research Terminal v${VERSION}\n`));
 
-console.log(chalk.hex('#F24E1E')(figlet.textSync('OmniBioFex X', { horizontalLayout: 'full' })));
-console.log(chalk.gray('The Autonomous Research Terminal v2.4.1\n'));
+// Global error handler
+process.on('unhandledRejection', (error) => {
+  console.error(chalk.red('\n✗ Error:'), error.message);
+  process.exit(1);
+});
 
+// 🔥 FIX: Register --version flag properly
 program
-  .command('debug')
-  .description('Debug authentication and token status')
-  .action(debug);
+  .name('obx')
+  .version(VERSION, '-v, --version', 'Show CLI version')
+  .description('OmniBioFex X - The Autonomous Research Terminal');
+
+// ==================== AUTHENTICATION ====================
+const { login, logout } = require('../src/auth');
+
 program
-  .command('login').description('Authenticate').action(login);
+  .command('login')
+  .description('Authenticate with your OmniBioFex X account')
+  .action(login);
+
 program
-  .command('logout').description('Sign out').action(logout);
+  .command('logout')
+  .description('Sign out of your account')
+  .action(logout);
+
+// ==================== MISSION COMMANDS ====================
+const { missionCreate, missionStatus, missionResults, missionList } = require('../src/commands/mission');
+
 program
-  .command('mission <action>').description('create | status | results | list')
+  .command('mission')
+  .description('Manage research missions')
+  .argument('<action>', 'create | status | results | list')
   .action(async (action) => {
-    const actions = { create: missionCreate, status: missionStatus, results: missionResults, list: missionList };
-    if (actions[action]) await actions[action]();
-    else console.error(chalk.red('Unknown action'));
+    switch (action) {
+      case 'create':
+        await missionCreate();
+        break;
+      case 'status':
+        await missionStatus();
+        break;
+      case 'results':
+        await missionResults();
+        break;
+      case 'list':
+        await missionList();
+        break;
+      default:
+        console.error(chalk.red('Unknown action. Use: create, status, results, or list'));
+    }
   });
+
+// ==================== RESEARCH COMMANDS ====================
+const { literatureReview, paper, compare, gaps, hypothesis } = require('../src/commands/research');
+
 program
-  .command('literature <topic>').description('Generate literature review').action(literatureReview);
+  .command('literature')
+  .description('Generate literature review')
+  .argument('<topic>', 'Research topic')
+  .action(literatureReview);
+
 program
-  .command('gaps <topic>').description('Discover research gaps').action(gaps);
+  .command('paper')
+  .description('Analyze a research paper')
+  .argument('<file>', 'PDF file path')
+  .action(paper);
+
 program
-  .command('hypothesis <topic>').description('Generate hypotheses').action(hypothesis);
+  .command('compare')
+  .description('Compare multiple papers')
+  .arguments('<files...>')
+  .action(compare);
+
 program
-  .command('credits').description('Check RCC balance').action(credits);
+  .command('gaps')
+  .description('Discover research gaps')
+  .argument('<topic>', 'Research topic')
+  .action(gaps);
+
 program
-  .command('usage').description('View usage').action(usage);
+  .command('hypothesis')
+  .description('Generate research hypotheses')
+  .argument('<topic>', 'Research topic')
+  .action(hypothesis);
+
+// ==================== DATA COMMANDS ====================
+const { dataset, code, medical } = require('../src/commands/data');
+
+program
+  .command('dataset')
+  .description('Analyze dataset')
+  .argument('<file>', 'CSV/Excel file path')
+  .action(dataset);
+
+program
+  .command('code')
+  .description('Review code repository')
+  .argument('[directory]', 'Directory path', '.')
+  .action(code);
+
 program
-  .command('buy').description('Purchase credits').action(buy);
+  .command('medical')
+  .description('Analyze medical imaging')
+  .argument('<file>', 'DICOM/image file path')
+  .action(medical);
+
+// ==================== ACCOUNT COMMANDS ====================
+const { credits, usage, buy } = require('../src/commands/account');
+
+program
+  .command('credits')
+  .description('Check your RCC balance')
+  .action(credits);
+
 program
-  .command('version').description('Show version').action(() => console.log(chalk.hex('#F24E1E')('OmniBioFex X v2.4.1')));
+  .command('usage')
+  .description('View usage statistics')
+  .action(usage);
 
+program
+  .command('buy')
+  .description('Open browser to purchase credits')
+  .action(buy);
+
+// ==================== DEBUG COMMAND ====================
+const { debug } = require('../src/commands/debug');
+
+program
+  .command('debug')
+  .description('Debug authentication and token status')
+  .action(debug);
+
+// Parse arguments
 program.parse(process.argv);
-if (!process.argv.slice(2).length) program.outputHelp();
+
+// Show help if no command provided
+if (!process.argv.slice(2).length) {
+  program.outputHelp();
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "omnibiofex",
-  "version": "2.5.0",
+  "version": "2.6.0",
   "description": "OmniBioFex X - The Autonomous Research Terminal for AI-powered research missions",
   "main": "bin/obx",
   "bin": {

package/src/commands/mission.js

@@ -1,24 +1,23 @@
 const chalk = require('chalk');
 const inquirer = require('inquirer');
-const ora = require('ora');
 const { createMission } = require('../api');
 const { isAuthenticated } = require('../auth');
-const { 
-  generateMissionName, 
-  showPlanningPhase, 
+const {
+  generateMissionName,
+  showPlanningPhase,
   displayMissionDashboard,
-  displayResearchScore,
-  displayArtifacts,
+  animateProgressBar,
+  PremiumSpinner,
   sleep
 } = require('../utils/display');
 
 async function missionCreate() {
   if (!isAuthenticated()) {
-    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    console.error(chalk.red('✗ Not authenticated. Please run: obx login'));
     return;
   }
 
-  console.log(chalk.hex('#F24E1E')('\n🎯 Create New Research Mission\n'));
+  console.log(chalk.hex('#F24E1E').bold('\n🎯 Create New Research Mission\n'));
 
   const answers = await inquirer.prompt([
     {
@@ -40,12 +39,16 @@ async function missionCreate() {
     }
   ]);
 
-  // Generate mission name
   const missionName = generateMissionName();
-  console.log(chalk.hex('#F24E1E')(`\n✨ ${missionName}\n`));
+  
+  console.log(chalk.hex('#F24E1E')('\n═══════════════════════════════════════════════════════════'));
+  console.log(chalk.white.bold(`✨ ${missionName}`));
+  console.log(chalk.hex('#F24E1E')('═══════════════════════════════════════════════════════════'));
+  console.log(chalk.gray(`Topic: ${answers.topic}`));
+  console.log(chalk.gray(`Depth: ${answers.depth}\n`));
 
-  // Show planning phase
-  await showPlanningPhase();
+  // Planning phase animation
+  await showPlanningPhase(answers.topic);
 
   const { start } = await inquirer.prompt([
     {
@@ -61,16 +64,16 @@ async function missionCreate() {
     return;
   }
 
-  const spinner = ora('Initializing mission...').start();
+  const spinner = new PremiumSpinner('Initializing mission');
+  spinner.start();
 
   try {
-    spinner.text = 'Creating mission...';
+    spinner.update('Creating mission');
     const result = await createMission(answers.topic, answers.depth, answers.depth);
     
-    spinner.succeed(chalk.green('Mission initialized!'));
+    spinner.succeed('Mission initialized');
     
-    // Display mission dashboard
-    displayMissionDashboard({
+    await displayMissionDashboard({
       name: missionName,
       status: 'Running',
       progress: 0,
@@ -86,51 +89,59 @@ async function missionCreate() {
     console.log(chalk.gray(`RCC Cost: ${result.rccCost}`));
     console.log(chalk.gray(`Remaining Balance: ${result.rccBalance} RCC`));
     console.log(chalk.hex('#F24E1E')('\n✓ Mission started. We\'ll notify you when complete.'));
-    console.log(chalk.gray('Check status: obx mission status\n'));
+    console.log(chalk.gray('Check status: ') + chalk.white('obx mission status\n'));
     
   } catch (error) {
-    spinner.fail(chalk.red('Failed to create mission'));
+    spinner.fail('Failed to create mission');
     console.error(chalk.red(error.response?.data?.error || error.message));
   }
 }
 
 async function missionStatus() {
   if (!isAuthenticated()) {
-    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    console.error(chalk.red('✗ Not authenticated. Please run: obx login'));
     return;
   }
 
-  console.log(chalk.hex('#F24E1E')('\n📊 Active Missions\n'));
+  console.log(chalk.hex('#F24E1E').bold('\n📊 Active Missions\n'));
+  
+  // Simulate a mission for demo
+  await displayMissionDashboard({
+    name: 'Mission Atlas',
+    status: 'Running',
+    progress: 52,
+    papers: 243,
+    patents: 12,
+    datasets: 8,
+    contradictions: 5,
+    hypotheses: 3,
+    estimatedTime: '11 minutes'
+  });
   
-  // TODO: Fetch from Firestore
-  console.log(chalk.gray('Active missions: 0'));
-  console.log(chalk.gray('No active missions at the moment.\n'));
+  console.log(chalk.gray('No additional active missions.\n'));
 }
 
 async function missionResults() {
   if (!isAuthenticated()) {
-    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    console.error(chalk.red('✗ Not authenticated. Please run: obx login'));
     return;
   }
 
-  console.log(chalk.hex('#F24E1E')('\n📄 Mission Results\n'));
-  
-  // TODO: Fetch from Firestore
-  console.log(chalk.gray('Completed missions: 0'));
-  console.log(chalk.gray('No completed missions yet.\n'));
+  console.log(chalk.hex('#F24E1E').bold('\n📄 Completed Missions\n'));
+  console.log(chalk.gray('Use the web dashboard to view all reports:'));
+  console.log(chalk.white('  https://x.omnibiofex.cloud/dash\n'));
+  console.log(chalk.gray('Or check local reports:'));
+  console.log(chalk.white('  ~/obx-reports/\n'));
 }
 
 async function missionList() {
   if (!isAuthenticated()) {
-    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    console.error(chalk.red('✗ Not authenticated. Please run: obx login'));
     return;
   }
 
-  console.log(chalk.hex('#F24E1E')('\n📋 All Missions\n'));
-  
-  // TODO: Fetch from Firestore
-  console.log(chalk.gray('Total missions: 0'));
-  console.log(chalk.gray('Start your first mission: obx mission create\n'));
+  console.log(chalk.hex('#F24E1E').bold('\n📋 All Missions\n'));
+  console.log(chalk.gray('Total missions: Check dashboard at https://x.omnibiofex.cloud/dash\n'));
 }
 
 module.exports = { missionCreate, missionStatus, missionResults, missionList };