docrev 0.11.3 → 0.12.0

package/lib/commands/doi.ts

@@ -1,451 +0,0 @@
-/**
- * DOI commands: doi, orcid
- *
- * Commands for DOI validation, fetching, and ORCID profile lookup.
- */
-
-import {
-  chalk,
-  fs,
-  path,
-  fmt,
-} from './context.js';
-import type { Command } from 'commander';
-
-interface DoiOptions {
-  bib: string;
-  strict?: boolean;
-  resolve?: boolean;
-  confidence: string;
-}
-
-interface OrcidOptions {
-  yaml?: boolean;
-  badge?: boolean;
-}
-
-/**
- * Register DOI commands with the program
- */
-export function register(program: Command): void {
-  // ==========================================================================
-  // DOI command - Validate and fetch DOIs
-  // ==========================================================================
-
-  program
-    .command('doi')
-    .description('Validate DOIs in bibliography or fetch citations from DOI')
-    .argument('<action>', 'Action: check, fetch, add, lookup')
-    .argument('[input]', 'DOI (for fetch/add) or .bib file (for check)')
-    .option('-b, --bib <file>', 'Bibliography file', 'references.bib')
-    .option('--strict', 'Fail on missing DOIs for articles')
-    .option('--no-resolve', 'Only check format, skip resolution check')
-    .option('--confidence <level>', 'Minimum confidence: high, medium, low (default: medium)', 'medium')
-    .action(async (action: string, input: string | undefined, options: DoiOptions) => {
-      const { parseBibEntries, checkBibDois, fetchBibtex, addToBib, isValidDoiFormat, lookupDoi, lookupMissingDois } = await import('../doi.js');
-
-      if (action === 'check') {
-        const bibPath = input || options.bib;
-
-        if (!fs.existsSync(bibPath)) {
-          console.error(fmt.status('error', `File not found: ${bibPath}`));
-          process.exit(1);
-        }
-
-        console.log(fmt.header(`DOI Check: ${path.basename(bibPath)}`));
-        console.log();
-
-        const spin = fmt.spinner('Validating DOIs...').start();
-
-        try {
-          const results = await checkBibDois(bibPath, {
-            checkMissing: options.strict,
-          });
-
-          spin.stop();
-
-          // Group results by status
-          const valid = results.entries.filter(e => e.status === 'valid');
-          const invalid = results.entries.filter(e => e.status === 'invalid');
-          const unreachable = results.entries.filter(e => e.status === 'unreachable');
-          const missing = results.entries.filter(e => e.status === 'missing');
-          const skipped = results.entries.filter(e => e.status === 'skipped');
-
-          // Summary table
-          const summaryRows: string[][] = [
-            [chalk.green('Valid'), chalk.green(valid.length.toString())],
-            [invalid.length > 0 ? chalk.red('Invalid') : 'Invalid', invalid.length > 0 ? chalk.red(invalid.length.toString()) : '0'],
-          ];
-          if (unreachable.length > 0) {
-            summaryRows.push([chalk.yellow('Unreachable'), chalk.yellow(unreachable.length.toString())]);
-          }
-          summaryRows.push(
-            [missing.length > 0 ? chalk.yellow('Missing (articles)') : 'Missing', missing.length > 0 ? chalk.yellow(missing.length.toString()) : '0'],
-            [chalk.dim('Skipped'), chalk.dim(skipped.length.toString())],
-          );
-          console.log(fmt.table(['Status', 'Count'], summaryRows));
-          console.log();
-
-          // Show invalid DOIs
-          if (invalid.length > 0) {
-            console.log(chalk.red('Invalid DOIs:'));
-            for (const e of invalid) {
-              console.log(`  ${chalk.bold(e.key)}: ${e.doi || 'N/A'}`);
-              console.log(chalk.dim(`    ${e.message}`));
-            }
-            console.log();
-          }
-
-          // Show unreachable DOIs (network issue — not necessarily invalid)
-          if (unreachable.length > 0) {
-            console.log(chalk.yellow('Unreachable (could not contact registry — DOI may be fine):'));
-            for (const e of unreachable) {
-              console.log(`  ${chalk.bold(e.key)}: ${e.doi || 'N/A'}`);
-              console.log(chalk.dim(`    ${e.message}`));
-            }
-            console.log();
-          }
-
-          // Show missing (articles without DOI)
-          if (missing.length > 0) {
-            console.log(chalk.yellow('Missing DOIs (should have DOI):'));
-            for (const e of missing) {
-              console.log(`  ${chalk.bold(e.key)} [${e.type}]`);
-              if (e.title) console.log(chalk.dim(`    "${e.title}"`));
-            }
-            console.log();
-          }
-
-          // Show skipped breakdown
-          if (skipped.length > 0) {
-            // Count by reason
-            const manualSkip = skipped.filter(e => e.message === 'Marked as no-doi');
-            const bookTypes = skipped.filter(e => e.message?.includes('typically has no DOI'));
-            const noField = skipped.filter(e => e.message === 'No DOI field');
-
-            console.log(chalk.dim('Skipped entries:'));
-            if (manualSkip.length > 0) {
-              console.log(chalk.dim(`  ${manualSkip.length} marked with nodoi={true}`));
-            }
-            if (bookTypes.length > 0) {
-              const types = [...new Set(bookTypes.map(e => e.type))].join(', ');
-              console.log(chalk.dim(`  ${bookTypes.length} by type (${types})`));
-            }
-            if (noField.length > 0) {
-              console.log(chalk.dim(`  ${noField.length} with no DOI field`));
-            }
-            console.log();
-          }
-
-          // Final status
-          if (invalid.length === 0 && missing.length === 0) {
-            console.log(fmt.status('success', 'All DOIs valid'));
-          } else if (invalid.length > 0) {
-            console.log(fmt.status('error', `${invalid.length} invalid DOI(s) found`));
-            if (options.strict) process.exit(1);
-          } else {
-            console.log(fmt.status('warning', `${missing.length} article(s) missing DOI`));
-          }
-
-          // Hint about skipping
-          console.log();
-          console.log(chalk.dim('To skip DOI check for an entry, add: nodoi = {true}'));
-          console.log(chalk.dim('Or add comment before entry: % no-doi'));
-
-        } catch (err) {
-          spin.stop();
-          const error = err as Error;
-          console.error(fmt.status('error', error.message));
-          process.exit(1);
-        }
-
-      } else if (action === 'fetch') {
-        if (!input) {
-          console.error(fmt.status('error', 'DOI required'));
-          console.log(chalk.dim('Usage: rev doi fetch 10.1234/example'));
-          process.exit(1);
-        }
-
-        const spin = fmt.spinner(`Fetching BibTeX for ${input}...`).start();
-
-        try {
-          const result = await fetchBibtex(input);
-
-          if (result.success) {
-            spin.success('BibTeX retrieved');
-            console.log();
-            console.log(result.bibtex);
-          } else {
-            spin.error(result.error!);
-            process.exit(1);
-          }
-        } catch (err) {
-          const error = err as Error;
-          spin.error(error.message);
-          process.exit(1);
-        }
-
-      } else if (action === 'add') {
-        if (!input) {
-          console.error(fmt.status('error', 'DOI required'));
-          console.log(chalk.dim('Usage: rev doi add 10.1234/example'));
-          process.exit(1);
-        }
-
-        const bibPath = options.bib;
-        const spin = fmt.spinner(`Fetching and adding ${input}...`).start();
-
-        try {
-          const fetchResult = await fetchBibtex(input);
-
-          if (!fetchResult.success) {
-            spin.error(fetchResult.error!);
-            process.exit(1);
-          }
-
-          const addResult = addToBib(bibPath, fetchResult.bibtex!);
-
-          if (addResult.success) {
-            spin.success(`Added @${addResult.key} to ${bibPath}`);
-          } else {
-            spin.error(addResult.error!);
-            process.exit(1);
-          }
-        } catch (err) {
-          const error = err as Error;
-          spin.error(error.message);
-          process.exit(1);
-        }
-
-      } else if (action === 'lookup') {
-        const bibPath = input || options.bib;
-
-        if (!fs.existsSync(bibPath)) {
-          console.error(fmt.status('error', `File not found: ${bibPath}`));
-          process.exit(1);
-        }
-
-        console.log(fmt.header(`DOI Lookup: ${path.basename(bibPath)}`));
-        console.log();
-
-        const entries = parseBibEntries(bibPath);
-        const missing = entries.filter(e => !e.doi && !e.skip && e.expectDoi);
-
-        if (missing.length === 0) {
-          console.log(fmt.status('success', 'No entries need DOI lookup'));
-          return;
-        }
-
-        console.log(chalk.dim(`Found ${missing.length} entries without DOIs to search...\n`));
-
-        let found = 0;
-        let notFound = 0;
-        let lowConfidence = 0;
-        const results: Array<{ entry: any; result: any; status: string }> = [];
-
-        for (let i = 0; i < missing.length; i++) {
-          const entry = missing[i];
-
-          // Extract first author last name
-          let author = '';
-          if (entry.authorRaw) {
-            const firstAuthor = entry.authorRaw.split(' and ')[0];
-            // Handle "Last, First" or "First Last" formats
-            if (firstAuthor.includes(',')) {
-              author = firstAuthor.split(',')[0].trim();
-            } else {
-              const parts = firstAuthor.trim().split(/\s+/);
-              author = parts[parts.length - 1]; // Last word is usually surname
-            }
-          }
-
-          process.stdout.write(`\r${chalk.dim(`[${i + 1}/${missing.length}]`)} ${entry.key}...`);
-
-          const result = await lookupDoi(entry.title, author, entry.year, entry.journal);
-
-          if (result.found) {
-            if (result.confidence === 'high') {
-              found++;
-              results.push({ entry, result, status: 'found' });
-            } else if (result.confidence === 'medium') {
-              found++;
-              results.push({ entry, result, status: 'found' });
-            } else {
-              lowConfidence++;
-              results.push({ entry, result, status: 'low' });
-            }
-          } else {
-            notFound++;
-            results.push({ entry, result, status: 'not-found' });
-          }
-
-          // Rate limiting
-          await new Promise(r => setTimeout(r, 200));
-        }
-
-        // Clear progress line
-        process.stdout.write('\r\x1B[K');
-
-        // Show results
-        console.log(fmt.table(
-          ['Status', 'Count'],
-          [
-            [chalk.green('Found (high/medium confidence)'), chalk.green(found.toString())],
-            [chalk.yellow('Found (low confidence)'), chalk.yellow(lowConfidence.toString())],
-            [chalk.dim('Not found'), chalk.dim(notFound.toString())],
-          ]
-        ));
-        console.log();
-
-        // Filter by confidence level
-        const confLevel = options.confidence || 'medium';
-        const confLevels: Record<string, number> = { high: 3, medium: 2, low: 1 };
-        const minConf = confLevels[confLevel] || 2;
-
-        const filteredResults = results.filter(r => {
-          if (r.status === 'not-found') return false;
-          const resultConf = confLevels[r.result.confidence] || 1;
-          return resultConf >= minConf;
-        });
-
-        const hiddenCount = results.filter(r => {
-          if (r.status === 'not-found') return false;
-          const resultConf = confLevels[r.result.confidence] || 1;
-          return resultConf < minConf;
-        }).length;
-
-        if (filteredResults.length > 0) {
-          console.log(chalk.cyan(`Found DOIs (${confLevel}+ confidence):`));
-          console.log();
-
-          for (const { entry, result } of filteredResults) {
-            const conf = result.confidence === 'high' ? chalk.green('●') :
-                         result.confidence === 'medium' ? chalk.yellow('●') :
-                         chalk.red('○');
-
-            // Check year match
-            const entryYear = entry.year;
-            const foundYear = result.metadata?.year;
-            const yearExact = entryYear && foundYear && entryYear === foundYear;
-            const yearClose = entryYear && foundYear && Math.abs(entryYear - foundYear) === 1;
-            const yearMismatch = entryYear && foundYear && Math.abs(entryYear - foundYear) > 1;
-
-            console.log(`  ${conf} ${chalk.bold(entry.key)} (${entryYear || '?'})`);
-            console.log(chalk.dim(`     Title: ${entry.title}`));
-            console.log(chalk.cyan(`     DOI: ${result.doi}`));
-
-            if (result.metadata?.journal) {
-              let yearDisplay: string;
-              if (yearExact) {
-                yearDisplay = chalk.green(`(${foundYear})`);
-              } else if (yearClose) {
-                yearDisplay = chalk.yellow(`(${foundYear}) ≈`);
-              } else if (yearMismatch) {
-                yearDisplay = chalk.red.bold(`(${foundYear}) ⚠ YEAR MISMATCH`);
-              } else {
-                yearDisplay = chalk.dim(`(${foundYear || '?'})`);
-              }
-              console.log(`     ${chalk.dim('Found:')} ${result.metadata.journal} ${yearDisplay}`);
-            }
-
-            // Extra warning for year mismatch
-            if (yearMismatch) {
-              console.log(chalk.red(`     ⚠ Expected ${entryYear}, found ${foundYear} - verify this is correct!`));
-            }
-
-            console.log();
-          }
-
-          // Offer to add DOIs
-          console.log(chalk.dim('To add a DOI to your .bib file:'));
-          console.log(chalk.dim('  1. Open references.bib'));
-          console.log(chalk.dim('  2. Add: doi = {10.xxxx/xxxxx}'));
-          console.log();
-          console.log(chalk.dim('Or use: rev doi add <doi> to fetch full BibTeX'));
-        }
-
-        // Show hidden count
-        if (hiddenCount > 0) {
-          console.log(chalk.yellow(`\n${hiddenCount} lower-confidence matches hidden.`));
-          if (confLevel === 'high') {
-            console.log(chalk.dim('Use --confidence medium or --confidence low to show more.'));
-          } else if (confLevel === 'medium') {
-            console.log(chalk.dim('Use --confidence low to show all matches.'));
-          }
-        }
-
-        // Show not found
-        if (notFound > 0) {
-          console.log(chalk.dim(`${notFound} entries could not be matched. These may be:`));
-          console.log(chalk.dim('  - Books, theses, or reports (often no DOI)'));
-          console.log(chalk.dim('  - Very old papers (pre-DOI era)'));
-          console.log(chalk.dim('  - Title mismatch (special characters, abbreviations)'));
-        }
-
-      } else {
-        console.error(fmt.status('error', `Unknown action: ${action}`));
-        console.log(chalk.dim('Actions: check, fetch, add, lookup'));
-        process.exit(1);
-      }
-    });
-
-  // ==========================================================================
-  // ORCID command - Fetch author info from ORCID
-  // ==========================================================================
-
-  program
-    .command('orcid')
-    .description('Fetch author information from ORCID')
-    .argument('<orcid>', 'ORCID iD (e.g., 0000-0002-1825-0097)')
-    .option('--yaml', 'Output as YAML for rev.yaml authors section')
-    .option('--badge', 'Output markdown badge')
-    .action(async (orcidInput: string, options: OrcidOptions) => {
-      const { fetchOrcidProfile, fetchOrcidWorkCount, formatAuthorYaml, getOrcidBadge, cleanOrcid, isValidOrcid } = await import('../orcid.js');
-
-      const orcid = cleanOrcid(orcidInput);
-
-      if (!isValidOrcid(orcid)) {
-        console.error(fmt.status('error', `Invalid ORCID format: ${orcidInput}`));
-        console.log(chalk.dim('Expected format: 0000-0000-0000-0000'));
-        console.log(chalk.dim('Or: https://orcid.org/0000-0000-0000-0000'));
-        process.exit(1);
-      }
-
-      console.log(chalk.cyan(`Fetching ORCID profile...`));
-
-      try {
-        const profile = await fetchOrcidProfile(orcid);
-        const workCount = await fetchOrcidWorkCount(orcid);
-
-        if (options.yaml) {
-          console.log();
-          console.log(formatAuthorYaml(profile));
-          return;
-        }
-
-        if (options.badge) {
-          console.log();
-          console.log(getOrcidBadge(orcid));
-          return;
-        }
-
-        console.log();
-        console.log(fmt.header('ORCID Profile'));
-        console.log();
-        console.log(`  ${chalk.bold('Name:')}        ${profile.name || chalk.dim('(not public)')}`);
-        console.log(`  ${chalk.bold('ORCID:')}       ${chalk.green(profile.orcid)}`);
-        console.log(`  ${chalk.bold('Affiliation:')} ${profile.affiliation || chalk.dim('(not public)')}`);
-        console.log(`  ${chalk.bold('Email:')}       ${profile.email || chalk.dim('(not public)')}`);
-        console.log(`  ${chalk.bold('Works:')}       ${workCount} publication(s)`);
-        console.log();
-        console.log(chalk.dim(`  Profile: https://orcid.org/${profile.orcid}`));
-        console.log();
-        console.log(chalk.dim('  Use --yaml to output for rev.yaml authors section'));
-        console.log(chalk.dim('  Use --badge to get markdown badge'));
-      } catch (err) {
-        const error = err as Error;
-        console.error(fmt.status('error', error.message));
-        process.exit(1);
-      }
-    });
-}