omnibiofex 2.5.1 → 2.6.1

package/src/commands/research.js

@@ -1,5 +1,4 @@
 const chalk = require('chalk');
-const ora = require('ora');
 const fs = require('fs');
 const path = require('path');
 const os = require('os');
@@ -8,345 +7,285 @@ const { isAuthenticated } = require('../auth');
 const {
   generateMissionName,
   animateResearchSources,
+  showPlanningPhase,
   displayMissionDashboard,
   displayResearchScore,
   displayArtifacts,
+  generateResearchScore,
+  generateArtifacts,
+  typeAIResponse,
+  sleep,
+  PremiumSpinner,
+  animateProgressBar
 } = require('../utils/display');
 
-// Create reports directory
 const REPORTS_DIR = path.join(os.homedir(), 'obx-reports');
 if (!fs.existsSync(REPORTS_DIR)) {
   fs.mkdirSync(REPORTS_DIR, { recursive: true });
 }
 
-/**
- * Save report to a Markdown file.
- * @param {string} topic - The research topic or file name.
- * @param {string} content - The report content.
- * @param {string} missionName - A unique, human‑readable mission name.
- * @returns {string} The path to the saved file.
- */
 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;
 }
 
-/**
- * Parse the research score from the AI response.
- * Looks for patterns like "Novelty: 81%", "Evidence: 93%", etc.
- * Falls back to sensible defaults if not found.
- */
-function parseResearchScore(response) {
-  const scoreMatch = response.match(
-    /Research Score[\s\S]*?Novelty[:\s]*(\d+)%[\s\S]*?Evidence[:\s]*(\d+)%[\s\S]*?Confidence[:\s]*(\d+)%/i
-  );
-
-  if (scoreMatch) {
-    return {
-      novelty: parseInt(scoreMatch[1]),
-      evidence: parseInt(scoreMatch[2]),
-      confidence: parseInt(scoreMatch[3]),
-      methodology: 85,
-      reproducibility: 88,
-      citations: 95,
-      gap: 'High',
-      publicationReady: true,
-    };
-  }
-
-  // Default fallback score
-  return {
-    novelty: 81,
-    evidence: 93,
-    confidence: 89,
-    methodology: 87,
-    reproducibility: 91,
-    citations: 96,
-    gap: 'High',
-    publicationReady: true,
-  };
-}
-
-/**
- * Extract the list of generated research artifacts from the AI response.
- */
-function parseArtifacts(response) {
-  const artifacts = [];
-
-  if (response.toLowerCase().includes('literature review')) {
-    artifacts.push('Literature Review');
-  }
-  if (response.toLowerCase().includes('timeline') || response.toLowerCase().includes('evolution')) {
-    artifacts.push('Research Timeline');
-  }
-  if (response.toLowerCase().includes('gap')) {
-    artifacts.push('Gap Analysis');
-  }
-  if (response.toLowerCase().includes('statistic')) {
-    artifacts.push('Statistical Summary');
-  }
-  if (response.toLowerCase().includes('citation')) {
-    artifacts.push('Citation Database');
-  }
-  if (response.toLowerCase().includes('hypothesis')) {
-    artifacts.push('Hypothesis Generator');
-  }
-
-  return artifacts.length > 0 ? artifacts : ['Research Report'];
-}
-
-// ============= COMMAND FUNCTIONS =============
-
+// ==================== LITERATURE REVIEW ====================
 async function literatureReview(topic) {
   if (!isAuthenticated()) {
-    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    console.error(chalk.red('✗ Not authenticated. Please run: obx login'));
     return;
   }
 
   const missionName = generateMissionName();
-  console.log(chalk.hex('#F24E1E')(`\n✨ ${missionName}\n`));
-
-  await animateResearchSources(['Nature', 'IEEE', 'PubMed', 'arXiv', 'Patents']);
-
-  const spinner = ora(`Generating literature review for: ${topic}`).start();
+  
+  // Header
+  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: Literature Review (100 RCC)\n`));
+
+  // Premium animations
+  await showPlanningPhase(topic);
+  await animateResearchSources();
+  
+  // Mission dashboard
+  await displayMissionDashboard({
+    name: missionName,
+    status: 'Running',
+    progress: 0,
+    papers: 0,
+    patents: 0,
+    datasets: 0,
+    estimatedTime: '3-5 minutes'
+  });
+
+  // API call with animated progress
+  const spinner = new PremiumSpinner('Executing multi-agent research');
+  spinner.start();
+  
+  let progressInterval = setInterval(() => {
+    // Just visual feedback
+  }, 1000);
 
   try {
     const result = await createMission(topic, 'LITERATURE_REVIEW');
-
-    spinner.succeed(chalk.green('Literature review complete!'));
-
+    
+    clearInterval(progressInterval);
+    spinner.succeed('Multi-agent research 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`));
-
-    displayMissionDashboard({
-      name: missionName,
-      status: 'Completed',
-      progress: 100,
-      papers: 412,
-      patents: 26,
-      datasets: 18,
-      contradictions: 14,
-      hypotheses: 7,
-    });
-
-    console.log(result.response);
-
-    const score = parseResearchScore(result.response);
-    displayResearchScore(score);
-
-    const artifacts = parseArtifacts(result.response);
-    displayArtifacts(artifacts);
-
+    console.log(chalk.gray(`💳 Remaining Balance: ${result.rccBalance} RCC`));
+
+    // Typing animation for the report
+    await typeAIResponse(result.response);
+    
+    // Research score
+    const score = generateResearchScore(result.response);
+    await displayResearchScore(score);
+    
+    // Artifacts
+    const artifacts = generateArtifacts('LITERATURE_REVIEW');
+    await displayArtifacts(artifacts);
+    
+    // Save to file
     const filepath = saveReport(topic, result.response, missionName);
     console.log(chalk.green(`✓ Report saved to: ${filepath}`));
-    console.log(chalk.gray('\nYou can now use all CLI commands.\n'));
+    console.log(chalk.gray('\nView with: cat ' + filepath + '\n'));
+    
   } catch (error) {
-    spinner.fail(chalk.red('Failed to generate literature review'));
+    clearInterval(progressInterval);
+    spinner.fail('Failed to generate literature review');
     console.error(chalk.red(error.response?.data?.error || error.message));
   }
 }
 
+// ==================== PAPER ANALYSIS ====================
 async function paper(file) {
   if (!isAuthenticated()) {
-    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    console.error(chalk.red('✗ Not authenticated. Please run: obx login'));
     return;
   }
 
-  const missionName = generateMissionName();
-  console.log(chalk.hex('#F24E1E')(`\n✨ ${missionName}\n`));
+  if (!fs.existsSync(file)) {
+    console.error(chalk.red(`✗ File not found: ${file}`));
+    return;
+  }
 
-  await animateResearchSources(['ArXiv', 'PubMed', 'Crossref']);
+  const missionName = generateMissionName();
+  console.log(chalk.hex('#F24E1E')(`\n✨ ${missionName}`));
+  console.log(chalk.gray(`Analyzing: ${file}\n`));
 
-  const spinner = ora(`Analyzing paper: ${file}`).start();
+  const spinner = new PremiumSpinner('Parsing document');
+  spinner.start();
 
   try {
-    const result = await createMission(`Analyze this paper: ${file}`, 'PAPER_ANALYSIS');
-
-    spinner.succeed(chalk.green('Paper analysis complete!'));
-
+    const fileContent = fs.readFileSync(file, 'utf8');
+    spinner.update('Extracting key claims');
+    await sleep(800);
+    
+    spinner.update('Evaluating methodology');
+    await sleep(800);
+    
+    spinner.succeed('Document parsed');
+
+    const result = await createMission(`Analyze this paper: ${fileContent.substring(0, 3000)}`, 'PAPER_ANALYSIS');
+    
     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`));
-
-    displayMissionDashboard({
-      name: missionName,
-      status: 'Completed',
-      progress: 100,
-      papers: 1,
-      patents: 0,
-      datasets: 0,
-      contradictions: 0,
-      hypotheses: 0,
-    });
-
-    console.log(result.response);
-
-    const score = parseResearchScore(result.response);
-    displayResearchScore(score);
-
-    const artifacts = parseArtifacts(result.response);
-    displayArtifacts(artifacts);
-
-    const filepath = saveReport(file, result.response, missionName);
-    console.log(chalk.green(`✓ Report saved to: ${filepath}\n`));
+    
+    await typeAIResponse(result.response);
+    
+    const score = generateResearchScore(result.response);
+    await displayResearchScore(score);
+    
   } catch (error) {
-    spinner.fail(chalk.red('Failed to analyze paper'));
+    spinner.fail('Failed to analyze paper');
     console.error(chalk.red(error.response?.data?.error || error.message));
   }
 }
 
+// ==================== COMPARE PAPERS ====================
 async function compare(files) {
   if (!isAuthenticated()) {
-    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    console.error(chalk.red('✗ Not authenticated. Please run: obx login'));
     return;
   }
 
-  const missionName = generateMissionName();
-  console.log(chalk.hex('#F24E1E')(`\n✨ ${missionName}\n`));
+  if (!files || files.length < 2) {
+    console.error(chalk.red('✗ Please provide at least 2 files to compare'));
+    return;
+  }
 
-  await animateResearchSources(['ArXiv', 'PubMed', 'Crossref', 'IEEE']);
+  const missionName = generateMissionName();
+  console.log(chalk.hex('#F24E1E')(`\n✨ ${missionName}`));
+  console.log(chalk.gray(`Comparing ${files.length} papers...\n`));
 
-  const spinner = ora(`Comparing ${files.length} papers`).start();
+  const spinner = new PremiumSpinner('Reading papers');
+  spinner.start();
 
   try {
-    const result = await createMission(
-      `Compare these papers: ${files.join(', ')}`,
-      'COMPARE_PAPERS'
-    );
-
-    spinner.succeed(chalk.green('Paper comparison complete!'));
-
+    const contents = files.map(f => {
+      if (!fs.existsSync(f)) {
+        console.error(chalk.red(`✗ File not found: ${f}`));
+        process.exit(1);
+      }
+      return fs.readFileSync(f, 'utf8').substring(0, 2000);
+    }).join('\n\n---\n\n');
+    
+    spinner.update('Detecting contradictions');
+    await sleep(1000);
+    
+    spinner.succeed('Papers analyzed');
+
+    const result = await createMission(`Compare these papers:\n${contents}`, 'PAPER_COMPARISON');
+    
     console.log(chalk.gray(`\n📊 Model: ${result.model}`));
     console.log(chalk.gray(`💰 RCC Cost: ${result.rccCost}`));
-    console.log(chalk.gray(`💳 Remaining Balance: ${result.rccBalance} RCC\n`));
-
-    displayMissionDashboard({
-      name: missionName,
-      status: 'Completed',
-      progress: 100,
-      papers: files.length,
-      patents: 0,
-      datasets: 0,
-      contradictions: 0,
-      hypotheses: 0,
-    });
-
-    console.log(result.response);
-
-    const score = parseResearchScore(result.response);
-    displayResearchScore(score);
-
-    const artifacts = parseArtifacts(result.response);
-    displayArtifacts(artifacts);
-
-    const filepath = saveReport(`comparison_${files.length}papers`, result.response, missionName);
-    console.log(chalk.green(`✓ Report saved to: ${filepath}\n`));
+    
+    await typeAIResponse(result.response);
+    
   } catch (error) {
-    spinner.fail(chalk.red('Failed to compare papers'));
+    spinner.fail('Failed to compare papers');
     console.error(chalk.red(error.response?.data?.error || error.message));
   }
 }
 
+// ==================== RESEARCH GAPS ====================
 async function gaps(topic) {
   if (!isAuthenticated()) {
-    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    console.error(chalk.red('✗ Not authenticated. Please run: obx login'));
     return;
   }
 
   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: ${topic}`));
+  console.log(chalk.gray(`Type: Research Gap Discovery (120 RCC)\n`));
 
-  await animateResearchSources(['Nature', 'IEEE', 'PubMed', 'arXiv']);
+  await showPlanningPhase(topic);
+  await animateResearchSources();
 
-  const spinner = ora(`Discovering research gaps for: ${topic}`).start();
+  const spinner = new PremiumSpinner('Mapping research landscape');
+  spinner.start();
 
   try {
     const result = await createMission(topic, 'RESEARCH_GAP');
-
-    spinner.succeed(chalk.green('Research gaps discovered!'));
-
+    
+    spinner.succeed('Research gaps discovered');
+    
     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`));
-
-    displayMissionDashboard({
-      name: missionName,
-      status: 'Completed',
-      progress: 100,
-      papers: 287,
-      patents: 19,
-      datasets: 12,
-      contradictions: 8,
-      hypotheses: 5,
-    });
-
-    console.log(result.response);
-
-    const score = parseResearchScore(result.response);
-    displayResearchScore(score);
-
-    const artifacts = parseArtifacts(result.response);
-    displayArtifacts(artifacts);
-
+    console.log(chalk.gray(`💳 Remaining Balance: ${result.rccBalance} RCC`));
+    
+    await typeAIResponse(result.response);
+    
+    const score = generateResearchScore(result.response);
+    await displayResearchScore(score);
+    
+    const artifacts = generateArtifacts('RESEARCH_GAP');
+    await displayArtifacts(artifacts);
+    
     const filepath = saveReport(topic, result.response, missionName);
     console.log(chalk.green(`✓ Report saved to: ${filepath}\n`));
+    
   } catch (error) {
-    spinner.fail(chalk.red('Failed to discover research gaps'));
+    spinner.fail('Failed to discover research gaps');
     console.error(chalk.red(error.response?.data?.error || error.message));
   }
 }
 
+// ==================== HYPOTHESIS GENERATION ====================
 async function hypothesis(topic) {
   if (!isAuthenticated()) {
-    console.error(chalk.red('Not authenticated. Please run: obx login'));
+    console.error(chalk.red('✗ Not authenticated. Please run: obx login'));
     return;
   }
 
   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: ${topic}`));
+  console.log(chalk.gray(`Type: Hypothesis Generation (100 RCC)\n`));
 
-  await animateResearchSources(['Nature', 'IEEE', 'PubMed']);
+  await showPlanningPhase(topic);
+  await animateResearchSources();
 
-  const spinner = ora(`Generating hypotheses for: ${topic}`).start();
+  const spinner = new PremiumSpinner('Generating hypotheses');
+  spinner.start();
 
   try {
     const result = await createMission(topic, 'HYPOTHESIS');
-
-    spinner.succeed(chalk.green('Hypotheses generated!'));
-
+    
+    spinner.succeed('Hypotheses 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`));
-
-    displayMissionDashboard({
-      name: missionName,
-      status: 'Completed',
-      progress: 100,
-      papers: 156,
-      patents: 8,
-      datasets: 5,
-      contradictions: 3,
-      hypotheses: 12,
-    });
-
-    console.log(result.response);
-
-    const score = parseResearchScore(result.response);
-    displayResearchScore(score);
-
-    const artifacts = parseArtifacts(result.response);
-    displayArtifacts(artifacts);
-
+    
+    await typeAIResponse(result.response);
+    
+    const score = generateResearchScore(result.response);
+    await displayResearchScore(score);
+    
+    const artifacts = generateArtifacts('HYPOTHESIS');
+    await displayArtifacts(artifacts);
+    
     const filepath = saveReport(topic, result.response, missionName);
     console.log(chalk.green(`✓ Report saved to: ${filepath}\n`));
+    
   } catch (error) {
-    spinner.fail(chalk.red('Failed to generate hypotheses'));
+    spinner.fail('Failed to generate hypotheses');
     console.error(chalk.red(error.response?.data?.error || error.message));
   }
 }