docrev 0.6.13 → 0.7.7

package/lib/commands/response.js

@@ -0,0 +1,374 @@
+/**
+ * Response commands: response, validate, profiles, anonymize
+ *
+ * Commands for generating reviewer responses and validating manuscripts.
+ */
+
+import {
+  chalk,
+  fs,
+  path,
+  fmt,
+  collectComments,
+  generateResponseLetter,
+  groupByReviewer,
+  getUserName,
+} from './context.js';
+
+/**
+ * Register response commands with the program
+ * @param {import('commander').Command} program
+ */
+export function register(program) {
+  // ==========================================================================
+  // RESPONSE command - Generate response letter for reviewers
+  // ==========================================================================
+
+  program
+    .command('response')
+    .description('Generate response letter from reviewer comments')
+    .argument('[files...]', 'Markdown files to process (default: all section files)')
+    .option('-o, --output <file>', 'Output file (default: response-letter.md)')
+    .option('-a, --author <name>', 'Author name for identifying replies')
+    .option('--no-context', 'Omit context snippets')
+    .option('--no-location', 'Omit file:line references')
+    .action(async (files, options) => {
+      let mdFiles = files;
+      if (!mdFiles || mdFiles.length === 0) {
+        const allFiles = fs.readdirSync('.').filter(f =>
+          f.endsWith('.md') && !['README.md', 'CLAUDE.md', 'paper.md'].includes(f)
+        );
+        mdFiles = allFiles;
+      }
+
+      if (mdFiles.length === 0) {
+        console.error(fmt.status('error', 'No markdown files found'));
+        process.exit(1);
+      }
+
+      const spin = fmt.spinner('Collecting comments...').start();
+
+      const comments = collectComments(mdFiles);
+      spin.stop();
+
+      if (comments.length === 0) {
+        console.log(fmt.status('info', 'No comments found in files'));
+        return;
+      }
+
+      const letter = generateResponseLetter(comments, {
+        authorName: options.author || getUserName() || 'Author',
+        includeContext: options.context !== false,
+        includeLocation: options.location !== false,
+      });
+
+      const outputPath = options.output || 'response-letter.md';
+      fs.writeFileSync(outputPath, letter, 'utf-8');
+
+      const grouped = groupByReviewer(comments);
+      const reviewers = [...grouped.keys()].filter(r =>
+        !r.toLowerCase().includes('claude') &&
+        r.toLowerCase() !== (options.author || '').toLowerCase()
+      );
+
+      console.log(fmt.header('Response Letter Generated'));
+      console.log();
+
+      const rows = reviewers.map(r => [r, grouped.get(r).length.toString()]);
+      console.log(fmt.table(['Reviewer', 'Comments'], rows));
+      console.log();
+      console.log(fmt.status('success', `Created ${outputPath}`));
+    });
+
+  // ==========================================================================
+  // VALIDATE command - Check manuscript against journal requirements
+  // ==========================================================================
+
+  program
+    .command('validate')
+    .description('Validate manuscript against journal requirements')
+    .argument('[files...]', 'Markdown files to validate (default: all section files)')
+    .option('-j, --journal <name>', 'Journal profile (e.g., nature, plos-one, science)')
+    .option('--list', 'List available journal profiles')
+    .action(async (files, options) => {
+      const { listJournals, validateProject, getJournalProfile } = await import('../journals.js');
+
+      if (options.list) {
+        console.log(fmt.header('Available Journal Profiles'));
+        console.log();
+        const journals = listJournals();
+        const builtIn = journals.filter(j => !j.custom);
+        const custom = journals.filter(j => j.custom);
+
+        for (const j of builtIn) {
+          console.log(`  ${chalk.bold(j.id)} - ${j.name}`);
+          if (j.url) console.log(chalk.dim(`    ${j.url}`));
+        }
+
+        if (custom.length > 0) {
+          console.log();
+          console.log(chalk.cyan('  Custom Profiles:'));
+          for (const j of custom) {
+            console.log(`  ${chalk.bold(j.id)} - ${j.name} ${chalk.cyan('[custom]')}`);
+            if (j.url) console.log(chalk.dim(`    ${j.url}`));
+          }
+        }
+
+        console.log();
+        console.log(chalk.dim('Usage: rev validate --journal <name>'));
+        console.log(chalk.dim('Manage custom profiles: rev profiles'));
+        return;
+      }
+
+      if (!options.journal) {
+        console.error(fmt.status('error', 'Please specify a journal with --journal <name>'));
+        console.error(chalk.dim('Use --list to see available profiles'));
+        process.exit(1);
+      }
+
+      const profile = getJournalProfile(options.journal);
+      if (!profile) {
+        console.error(fmt.status('error', `Unknown journal: ${options.journal}`));
+        console.error(chalk.dim('Use --list to see available profiles'));
+        process.exit(1);
+      }
+
+      let mdFiles = files;
+      if (!mdFiles || mdFiles.length === 0) {
+        mdFiles = fs.readdirSync('.').filter(f =>
+          f.endsWith('.md') && !['README.md', 'CLAUDE.md', 'paper.md'].includes(f)
+        );
+      }
+
+      if (mdFiles.length === 0) {
+        console.error(fmt.status('error', 'No markdown files found'));
+        process.exit(1);
+      }
+
+      console.log(fmt.header(`Validating for ${profile.name}`));
+      console.log(chalk.dim(`  ${profile.url}`));
+      console.log();
+
+      const result = validateProject(mdFiles, options.journal);
+
+      console.log(chalk.cyan('Manuscript Stats:'));
+      console.log(fmt.table(['Metric', 'Value'], [
+        ['Word count', result.stats.wordCount.toString()],
+        ['Abstract', `${result.stats.abstractWords} words`],
+        ['Title', `${result.stats.titleChars} chars`],
+        ['Figures', result.stats.figures.toString()],
+        ['Tables', result.stats.tables.toString()],
+        ['References', result.stats.references.toString()],
+      ]));
+      console.log();
+
+      if (result.errors.length > 0) {
+        console.log(chalk.red('Errors:'));
+        for (const err of result.errors) {
+          console.log(chalk.red(`  ✗ ${err}`));
+        }
+        console.log();
+      }
+
+      if (result.warnings.length > 0) {
+        console.log(chalk.yellow('Warnings:'));
+        for (const warn of result.warnings) {
+          console.log(chalk.yellow(`  ⚠ ${warn}`));
+        }
+        console.log();
+      }
+
+      if (result.valid) {
+        console.log(fmt.status('success', `Manuscript meets ${profile.name} requirements`));
+      } else {
+        console.log(fmt.status('error', `Manuscript has ${result.errors.length} error(s)`));
+        process.exit(1);
+      }
+    });
+
+  // ==========================================================================
+  // PROFILES command - Manage custom journal profiles
+  // ==========================================================================
+
+  program
+    .command('profiles')
+    .description('Manage custom journal profiles')
+    .option('--list', 'List all custom profiles')
+    .option('--new <name>', 'Create a new profile template')
+    .option('--project', 'Create profile in project directory (with --new)')
+    .option('--dirs', 'Show profile directory locations')
+    .action(async (options) => {
+      const {
+        listCustomProfiles,
+        saveProfileTemplate,
+        getPluginDirs,
+      } = await import('../plugins.js');
+      const { listJournals } = await import('../journals.js');
+
+      if (options.dirs) {
+        const dirs = getPluginDirs();
+        console.log(fmt.header('Profile Directories'));
+        console.log();
+        console.log(`  User:    ${dirs.user}`);
+        console.log(chalk.dim(`           ${dirs.userExists ? 'exists' : 'not created'}`));
+        console.log();
+        console.log(`  Project: ${dirs.project}`);
+        console.log(chalk.dim(`           ${dirs.projectExists ? 'exists' : 'not created'}`));
+        console.log();
+        console.log(chalk.dim('Use --new <name> to create a profile template'));
+        return;
+      }
+
+      if (options.new) {
+        try {
+          const filePath = saveProfileTemplate(options.new, options.project);
+          console.log(fmt.status('success', `Created profile template: ${filePath}`));
+          console.log(chalk.dim('Edit the file to customize journal requirements'));
+        } catch (err) {
+          console.error(fmt.status('error', err.message));
+          process.exit(1);
+        }
+        return;
+      }
+
+      console.log(fmt.header('Custom Journal Profiles'));
+      console.log();
+
+      const customProfiles = listCustomProfiles();
+
+      if (customProfiles.length === 0) {
+        console.log(chalk.dim('  No custom profiles found'));
+        console.log();
+        console.log(chalk.dim('  Create one with: rev profiles --new "Journal Name"'));
+        console.log();
+        const dirs = getPluginDirs();
+        console.log(chalk.dim(`  User profiles:    ${dirs.user}`));
+        console.log(chalk.dim(`  Project profiles: ${dirs.project}`));
+      } else {
+        for (const p of customProfiles) {
+          const source = p.source === 'project' ? chalk.cyan('[project]') : chalk.dim('[user]');
+          console.log(`  ${chalk.bold(p.id)} - ${p.name} ${source}`);
+          console.log(chalk.dim(`    ${p.path}`));
+        }
+        console.log();
+        console.log(chalk.dim(`  ${customProfiles.length} custom profile(s)`));
+      }
+
+      console.log();
+
+      const allJournals = listJournals();
+      const builtIn = allJournals.filter(j => !j.custom).length;
+      console.log(chalk.dim(`  ${builtIn} built-in profiles available (rev validate --list)`));
+    });
+
+  // ==========================================================================
+  // ANONYMIZE command - Prepare document for blind review
+  // ==========================================================================
+
+  program
+    .command('anonymize')
+    .description('Prepare document for blind review')
+    .argument('<input>', 'Input markdown file or directory')
+    .option('-o, --output <file>', 'Output file (default: input-anonymous.md)')
+    .option('--authors <names>', 'Author names to redact (comma-separated)')
+    .option('--dry-run', 'Show what would be changed without writing')
+    .action(async (input, options) => {
+      const { default: YAML } = await import('yaml');
+
+      const isDir = fs.existsSync(input) && fs.statSync(input).isDirectory();
+      const files = isDir
+        ? fs.readdirSync(input)
+            .filter(f => f.endsWith('.md') && !['README.md', 'CLAUDE.md'].includes(f))
+            .map(f => path.join(input, f))
+        : [input];
+
+      if (files.length === 0) {
+        console.error(fmt.status('error', 'No markdown files found'));
+        process.exit(1);
+      }
+
+      let authorNames = [];
+      if (options.authors) {
+        authorNames = options.authors.split(',').map(n => n.trim());
+      } else {
+        const configPath = isDir ? path.join(input, 'rev.yaml') : 'rev.yaml';
+        if (fs.existsSync(configPath)) {
+          try {
+            const config = YAML.parse(fs.readFileSync(configPath, 'utf-8'));
+            if (config.authors) {
+              authorNames = config.authors.map(a => typeof a === 'string' ? a : a.name).filter(Boolean);
+            }
+          } catch { /* ignore */ }
+        }
+      }
+
+      console.log(fmt.header('Anonymizing Document'));
+      console.log();
+
+      let totalChanges = 0;
+
+      for (const file of files) {
+        if (!fs.existsSync(file)) {
+          console.error(chalk.yellow(`  Skipping: ${file} (not found)`));
+          continue;
+        }
+
+        let text = fs.readFileSync(file, 'utf-8');
+        let changes = 0;
+
+        text = text.replace(/^---\n([\s\S]*?)\n---/, (match, fm) => {
+          let modified = fm;
+          modified = modified.replace(/^author:.*(?:\n(?:  |\t).*)*$/m, '');
+          modified = modified.replace(/^authors:.*(?:\n(?:  |\t|-\s+).*)*$/m, '');
+          modified = modified.replace(/^affiliation:.*$/m, '');
+          modified = modified.replace(/^email:.*$/m, '');
+          if (modified !== fm) changes++;
+          return '---\n' + modified.replace(/\n{3,}/g, '\n\n').trim() + '\n---';
+        });
+
+        const ackPatterns = [
+          /^#+\s*Acknowledgments?[\s\S]*?(?=^#|\Z)/gmi,
+          /^#+\s*Funding[\s\S]*?(?=^#|\Z)/gmi,
+        ];
+        for (const pattern of ackPatterns) {
+          const before = text;
+          text = text.replace(pattern, '');
+          if (text !== before) changes++;
+        }
+
+        for (const name of authorNames) {
+          const namePattern = new RegExp(`\\b${name.replace(/[.*+?^${}()|[\]\\]/g, '\\$&')}\\b`, 'gi');
+          const before = text;
+          text = text.replace(namePattern, '[AUTHOR]');
+          if (text !== before) changes++;
+        }
+
+        for (const name of authorNames) {
+          const lastName = name.split(/\s+/).pop();
+          if (lastName && lastName.length > 2) {
+            const citePat = new RegExp(`@${lastName}(\\d{4})`, 'gi');
+            const before = text;
+            text = text.replace(citePat, '@AUTHOR$1');
+            if (text !== before) changes++;
+          }
+        }
+
+        totalChanges += changes;
+
+        if (options.dryRun) {
+          console.log(chalk.dim(`  ${path.basename(file)}: ${changes} change(s)`));
+        } else {
+          const outPath = options.output || file.replace(/\.md$/, '-anonymous.md');
+          fs.writeFileSync(outPath, text, 'utf-8');
+          console.log(fmt.status('success', `${path.basename(file)} → ${path.basename(outPath)} (${changes} changes)`));
+        }
+      }
+
+      console.log();
+      if (options.dryRun) {
+        console.log(chalk.dim(`  Total: ${totalChanges} change(s) would be made`));
+      } else {
+        console.log(fmt.status('success', `Anonymized ${files.length} file(s)`));
+      }
+    });
+}