docrev 0.6.13 → 0.7.6

package/lib/commands/doi.js

@@ -0,0 +1,419 @@
+/**
+ * DOI commands: doi, orcid
+ *
+ * Commands for DOI validation, fetching, and ORCID profile lookup.
+ */
+
+import {
+  chalk,
+  fs,
+  path,
+  fmt,
+} from './context.js';
+
+/**
+ * Register DOI commands with the program
+ * @param {import('commander').Command} program
+ */
+export function register(program) {
+  // ==========================================================================
+  // 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, input, options) => {
+      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 missing = results.entries.filter(e => e.status === 'missing');
+          const skipped = results.entries.filter(e => e.status === 'skipped');
+
+          // Summary table
+          const summaryRows = [
+            [chalk.green('Valid'), chalk.green(valid.length.toString())],
+            [invalid.length > 0 ? chalk.red('Invalid') : 'Invalid', invalid.length > 0 ? chalk.red(invalid.length.toString()) : '0'],
+            [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 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();
+          console.error(fmt.status('error', err.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) {
+          spin.error(err.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) {
+          spin.error(err.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 ${missing.length} entries without DOIs to search...\n`));
+
+        let found = 0;
+        let notFound = 0;
+        let lowConfidence = 0;
+        const results = [];
+
+        for (let i = 0; i < missing.length; i++) {
+          const entry = missing[i];
+
+          // Extract first author last name
+          let author = '';
+          if (entry.authorRaw) {
+            const firstAuthor = entry.authorRaw.split(' and ')[0];
+            // Handle "Last, First" or "First Last" formats
+            if (firstAuthor.includes(',')) {
+              author = firstAuthor.split(',')[0].trim();
+            } else {
+              const parts = firstAuthor.trim().split(/\s+/);
+              author = parts[parts.length - 1]; // Last word is usually surname
+            }
+          }
+
+          process.stdout.write(`\r${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 = { 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: ${result.doi}`));
+
+            if (result.metadata?.journal) {
+              let yearDisplay;
+              if (yearExact) {
+                yearDisplay = chalk.green(`(${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, options) => {
+      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) {
+        console.error(fmt.status('error', err.message));
+        process.exit(1);
+      }
+    });
+}