docrev 0.8.1 → 0.8.5

package/dist/lib/commands/doi.js

@@ -0,0 +1,373 @@
+/**
+ * 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
+ */
+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();
+                const error = err;
+                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;
+                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;
+                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 ${missing.length} entries without DOIs to search...\n`));
+            let found = 0;
+            let notFound = 0;
+            let lowConfidence = 0;
+            const results = [];
+            for (let i = 0; i < missing.length; i++) {
+                const entry = missing[i];
+                // Extract first author last name
+                let author = '';
+                if (entry.authorRaw) {
+                    const firstAuthor = entry.authorRaw.split(' and ')[0];
+                    // Handle "Last, First" or "First Last" formats
+                    if (firstAuthor.includes(',')) {
+                        author = firstAuthor.split(',')[0].trim();
+                    }
+                    else {
+                        const parts = firstAuthor.trim().split(/\s+/);
+                        author = parts[parts.length - 1]; // Last word is usually surname
+                    }
+                }
+                process.stdout.write(`\r${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) {
+            const error = err;
+            console.error(fmt.status('error', error.message));
+            process.exit(1);
+        }
+    });
+}
+//# sourceMappingURL=doi.js.map

package/dist/lib/commands/doi.js.map

@@ -0,0 +1 @@
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package/dist/lib/commands/history.d.ts

@@ -0,0 +1,11 @@
+/**
+ * History commands: diff, history, contributors
+ *
+ * Commands for git-based revision tracking and author statistics.
+ */
+import type { Command } from 'commander';
+/**
+ * Register history commands with the program
+ */
+export declare function register(program: Command): void;
+//# sourceMappingURL=history.d.ts.map

package/dist/lib/commands/history.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"history.d.ts","sourceRoot":"","sources":["../../../lib/commands/history.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAsBzC;;GAEG;AACH,wBAAgB,QAAQ,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAgS/C"}