docrev 0.8.1 → 0.8.5

package/lib/journals.ts

@@ -0,0 +1,505 @@
+/**
+ * Journal validation profiles
+ * Check manuscripts against journal-specific requirements
+ */
+
+import * as fs from 'fs';
+import * as path from 'path';
+import type { JournalProfile, JournalRequirements, ValidationResult } from './types.js';
+import { loadCustomProfiles } from './plugins.js';
+import { countWords } from './utils.js';
+
+/**
+ * Journal requirement profiles
+ * Based on publicly available author guidelines
+ */
+export const JOURNAL_PROFILES: Record<string, JournalProfile> = {
+  nature: {
+    name: 'Nature',
+    url: 'https://www.nature.com/nature/for-authors',
+    requirements: {
+      wordLimit: { main: 3000, abstract: 150 },
+      references: { max: 50, doiRequired: true },
+      figures: { max: 6 },
+      sections: ['Abstract', 'Introduction', 'Results', 'Discussion', 'Methods'],
+    },
+  },
+
+  science: {
+    name: 'Science',
+    url: 'https://www.science.org/content/page/instructions-preparing-initial-manuscript',
+    requirements: {
+      wordLimit: { main: 2500, abstract: 125 },
+      references: { max: 40, doiRequired: true },
+      figures: { max: 4 },
+      sections: ['Abstract', 'Introduction', 'Results', 'Discussion'],
+    },
+  },
+
+  'plos-one': {
+    name: 'PLOS ONE',
+    url: 'https://journals.plos.org/plosone/s/submission-guidelines',
+    requirements: {
+      wordLimit: { abstract: 300 },
+      references: { doiRequired: false },
+      sections: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
+    },
+  },
+
+  'pnas': {
+    name: 'PNAS',
+    url: 'https://www.pnas.org/author-center/submitting-your-manuscript',
+    requirements: {
+      wordLimit: { main: 4500, abstract: 250 },
+      references: { max: 50, doiRequired: true },
+      figures: { max: 6 },
+      sections: ['Abstract', 'Introduction', 'Results', 'Discussion'],
+    },
+  },
+
+  'ecology-letters': {
+    name: 'Ecology Letters',
+    url: 'https://onlinelibrary.wiley.com/page/journal/14610248/homepage/forauthors.html',
+    requirements: {
+      wordLimit: { main: 5000, abstract: 150 },
+      references: { max: 50, doiRequired: true },
+      figures: { max: 6 },
+      sections: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
+    },
+  },
+
+  'ecological-applications': {
+    name: 'Ecological Applications',
+    url: 'https://esajournals.onlinelibrary.wiley.com/hub/journal/19395582/author-guidelines',
+    requirements: {
+      wordLimit: { main: 7000, abstract: 350 },
+      references: { doiRequired: true },
+      sections: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
+    },
+  },
+
+  'molecular-ecology': {
+    name: 'Molecular Ecology',
+    url: 'https://onlinelibrary.wiley.com/page/journal/1365294x/homepage/forauthors.html',
+    requirements: {
+      wordLimit: { main: 8000, abstract: 250 },
+      references: { doiRequired: true },
+      figures: { max: 8 },
+      sections: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
+    },
+  },
+
+  'elife': {
+    name: 'eLife',
+    url: 'https://reviewer.elifesciences.org/author-guide/full',
+    requirements: {
+      wordLimit: { abstract: 150 },
+      references: { doiRequired: true },
+      sections: ['Abstract', 'Introduction', 'Results', 'Discussion', 'Methods'],
+    },
+  },
+
+  'cell': {
+    name: 'Cell',
+    url: 'https://www.cell.com/cell/authors',
+    requirements: {
+      wordLimit: { main: 7000, abstract: 150 },
+      references: { max: 100, doiRequired: true },
+      figures: { max: 7 },
+      sections: ['Abstract', 'Introduction', 'Results', 'Discussion'],
+    },
+  },
+
+  'current-biology': {
+    name: 'Current Biology',
+    url: 'https://www.cell.com/current-biology/authors',
+    requirements: {
+      wordLimit: { main: 5000, abstract: 150 },
+      references: { max: 60, doiRequired: true },
+      figures: { max: 4 },
+      sections: ['Summary', 'Results', 'Discussion'],
+    },
+  },
+
+  'conservation-biology': {
+    name: 'Conservation Biology',
+    url: 'https://conbio.onlinelibrary.wiley.com/hub/journal/15231739/homepage/forauthors.html',
+    requirements: {
+      wordLimit: { main: 7000, abstract: 300 },
+      references: { doiRequired: true },
+      figures: { max: 6 },
+      sections: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
+    },
+  },
+
+  'biological-conservation': {
+    name: 'Biological Conservation',
+    url: 'https://www.elsevier.com/journals/biological-conservation/0006-3207/guide-for-authors',
+    requirements: {
+      wordLimit: { main: 8000, abstract: 400 },
+      references: { doiRequired: true },
+      sections: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
+    },
+  },
+
+  'journal-of-ecology': {
+    name: 'Journal of Ecology',
+    url: 'https://besjournals.onlinelibrary.wiley.com/hub/journal/13652745/author-guidelines',
+    requirements: {
+      wordLimit: { main: 7000, abstract: 350 },
+      references: { doiRequired: true },
+      sections: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
+    },
+  },
+
+  'functional-ecology': {
+    name: 'Functional Ecology',
+    url: 'https://besjournals.onlinelibrary.wiley.com/hub/journal/13652435/author-guidelines',
+    requirements: {
+      wordLimit: { main: 7000, abstract: 350 },
+      references: { doiRequired: true },
+      sections: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
+    },
+  },
+
+  'global-change-biology': {
+    name: 'Global Change Biology',
+    url: 'https://onlinelibrary.wiley.com/page/journal/13652486/homepage/forauthors.html',
+    requirements: {
+      wordLimit: { main: 7000, abstract: 300 },
+      references: { doiRequired: true },
+      figures: { max: 8 },
+      sections: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
+    },
+  },
+
+  'oikos': {
+    name: 'Oikos',
+    url: 'https://nsojournals.onlinelibrary.wiley.com/hub/journal/16000706/author-guidelines',
+    requirements: {
+      wordLimit: { main: 8000, abstract: 350 },
+      references: { doiRequired: true },
+      sections: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
+    },
+  },
+
+  'oecologia': {
+    name: 'Oecologia',
+    url: 'https://www.springer.com/journal/442/submission-guidelines',
+    requirements: {
+      wordLimit: { main: 8000, abstract: 250 },
+      references: { doiRequired: true },
+      sections: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
+    },
+  },
+
+  'biological-invasions': {
+    name: 'Biological Invasions',
+    url: 'https://www.springer.com/journal/10530/submission-guidelines',
+    requirements: {
+      wordLimit: { abstract: 250 },
+      references: { doiRequired: true },
+      sections: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
+    },
+  },
+
+  'diversity-distributions': {
+    name: 'Diversity and Distributions',
+    url: 'https://onlinelibrary.wiley.com/page/journal/14724642/homepage/forauthors.html',
+    requirements: {
+      wordLimit: { main: 6000, abstract: 300 },
+      references: { doiRequired: true },
+      figures: { max: 6 },
+      sections: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
+    },
+  },
+
+  'neobiota': {
+    name: 'NeoBiota',
+    url: 'https://neobiota.pensoft.net/about#Author_Guidelines',
+    requirements: {
+      wordLimit: { abstract: 350 },
+      references: { doiRequired: true },
+      sections: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
+    },
+  },
+
+  'peerj': {
+    name: 'PeerJ',
+    url: 'https://peerj.com/about/author-instructions/',
+    requirements: {
+      wordLimit: { abstract: 500 },
+      references: { doiRequired: false },
+      sections: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
+    },
+  },
+};
+
+/**
+ * Get all profiles (built-in + custom)
+ * Custom profiles override built-in ones with the same ID
+ */
+function getAllProfiles(): Record<string, JournalProfile> {
+  const customProfiles = loadCustomProfiles() as Record<string, JournalProfile>;
+  return { ...JOURNAL_PROFILES, ...customProfiles };
+}
+
+interface ListJournalsOptions {
+  includeCustom?: boolean;
+  customOnly?: boolean;
+}
+
+interface JournalListItem {
+  id: string;
+  name: string;
+  url: string;
+  custom?: boolean;
+}
+
+/**
+ * List all available journal profiles
+ */
+export function listJournals(options: ListJournalsOptions = {}): JournalListItem[] {
+  const { includeCustom = true, customOnly = false } = options;
+
+  const profiles = customOnly
+    ? (loadCustomProfiles() as Record<string, JournalProfile>)
+    : includeCustom
+      ? getAllProfiles()
+      : JOURNAL_PROFILES;
+
+  return Object.entries(profiles).map(([id, profile]) => ({
+    id,
+    name: profile.name,
+    url: profile.url,
+    custom: (profile as any).custom || false,
+  }));
+}
+
+/**
+ * Get a specific journal profile
+ */
+export function getJournalProfile(journalId: string): JournalProfile | null {
+  const normalized = journalId.toLowerCase().replace(/\s+/g, '-');
+  const profiles = getAllProfiles();
+  return profiles[normalized] || null;
+}
+
+
+/**
+ * Extract abstract from markdown
+ */
+function extractAbstract(text: string): string | null {
+  // Try to find abstract section
+  const patterns = [
+    /^#+\s*Abstract\s*\n([\s\S]*?)(?=^#+|\Z)/mi,
+    /^Abstract[:\s]*\n([\s\S]*?)(?=^#+|\n\n)/mi,
+  ];
+
+  for (const pattern of patterns) {
+    const match = text.match(pattern);
+    if (match && match[1]) {
+      return match[1].trim();
+    }
+  }
+
+  return null;
+}
+
+/**
+ * Extract title from markdown
+ */
+function extractTitle(text: string): string | null {
+  // Try YAML frontmatter
+  const yamlMatch = text.match(/^---\n[\s\S]*?title:\s*["']?([^"'\n]+)["']?[\s\S]*?\n---/m);
+  if (yamlMatch && yamlMatch[1]) {
+    return yamlMatch[1].trim();
+  }
+
+  // Try first H1
+  const h1Match = text.match(/^#\s+(.+)$/m);
+  if (h1Match && h1Match[1]) {
+    return h1Match[1].trim();
+  }
+
+  return null;
+}
+
+/**
+ * Extract sections from markdown
+ */
+function extractSections(text: string): string[] {
+  const sections: string[] = [];
+  const headerPattern = /^#+\s+(.+)$/gm;
+  let match: RegExpExecArray | null;
+
+  while ((match = headerPattern.exec(text)) !== null) {
+    if (match[1]) {
+      sections.push(match[1].trim());
+    }
+  }
+
+  return sections;
+}
+
+/**
+ * Count figures in markdown
+ */
+function countFigures(text: string): number {
+  // Count images with figure captions
+  const figurePattern = /!\[.*?\]\(.*?\)(\{#fig:[^}]+\})?/g;
+  const matches = text.match(figurePattern) || [];
+  return matches.length;
+}
+
+/**
+ * Count tables in markdown
+ */
+function countTables(text: string): number {
+  // Count tables (lines starting with |)
+  const tablePattern = /^\|[^|]+\|/gm;
+  const matches = text.match(tablePattern) || [];
+  // Divide by approximate rows per table
+  return Math.ceil(matches.length / 5);
+}
+
+/**
+ * Count references/citations in markdown
+ */
+function countReferences(text: string): number {
+  // Count unique citation keys
+  const citationPattern = /@(\w+)/g;
+  const citations = new Set<string>();
+  let match: RegExpExecArray | null;
+
+  while ((match = citationPattern.exec(text)) !== null) {
+    // Exclude cross-refs like @fig:label
+    if (match[1] && !match[0].includes(':')) {
+      citations.add(match[1]);
+    }
+  }
+
+  return citations.size;
+}
+
+interface ManuscriptStats {
+  wordCount: number;
+  abstractWords: number;
+  titleChars: number;
+  figures: number;
+  tables: number;
+  references: number;
+  sections: number;
+}
+
+interface ManuscriptValidationResult {
+  valid: boolean;
+  errors: string[];
+  warnings: string[];
+  stats: ManuscriptStats | null;
+  journal?: string;
+  url?: string;
+}
+
+/**
+ * Validate manuscript against journal requirements
+ */
+export function validateManuscript(text: string, journalId: string): ManuscriptValidationResult {
+  const profile = getJournalProfile(journalId);
+
+  if (!profile) {
+    return {
+      valid: false,
+      errors: [`Unknown journal: ${journalId}`],
+      warnings: [],
+      stats: null,
+    };
+  }
+
+  const req = profile.requirements;
+  const errors: string[] = [];
+  const warnings: string[] = [];
+
+  // Extract content
+  const abstract = extractAbstract(text);
+  const title = extractTitle(text);
+  const sections = extractSections(text);
+  const mainWordCount = countWords(text);
+  const figureCount = countFigures(text);
+  const tableCount = countTables(text);
+  const refCount = countReferences(text);
+
+  const stats: ManuscriptStats = {
+    wordCount: mainWordCount,
+    abstractWords: abstract ? countWords(abstract) : 0,
+    titleChars: title ? title.length : 0,
+    figures: figureCount,
+    tables: tableCount,
+    references: refCount,
+    sections: sections.length,
+  };
+
+  // Word limits
+  if (req.wordLimit) {
+    if (req.wordLimit.main && mainWordCount > req.wordLimit.main) {
+      errors.push(`Main text exceeds ${req.wordLimit.main} words (current: ${mainWordCount})`);
+    }
+    if (req.wordLimit.abstract && abstract) {
+      const absWords = countWords(abstract);
+      if (absWords > req.wordLimit.abstract) {
+        errors.push(`Abstract exceeds ${req.wordLimit.abstract} words (current: ${absWords})`);
+      }
+    }
+  }
+
+  // References
+  if (req.references) {
+    if (req.references.max && refCount > req.references.max) {
+      errors.push(`References exceed ${req.references.max} (current: ${refCount})`);
+    }
+    if (req.references.doiRequired) {
+      warnings.push('DOI required for all references - run "rev doi check" to verify');
+    }
+  }
+
+  // Figures/tables
+  if (req.figures) {
+    if (req.figures.max && figureCount > req.figures.max) {
+      errors.push(`Figures exceed ${req.figures.max} (current: ${figureCount})`);
+    }
+  }
+
+  // Required sections
+  if (req.sections) {
+    for (const reqSection of req.sections) {
+      const found = sections.some(s =>
+        s.toLowerCase().includes(reqSection.toLowerCase())
+      );
+      if (!found) {
+        warnings.push(`Missing required section: ${reqSection}`);
+      }
+    }
+  }
+
+  return {
+    valid: errors.length === 0,
+    errors,
+    warnings,
+    stats,
+    journal: profile.name,
+    url: profile.url,
+  };
+}
+
+/**
+ * Validate multiple files against journal requirements
+ */
+export function validateProject(files: string[], journalId: string): ManuscriptValidationResult {
+  // Combine all file contents
+  const combined = files
+    .filter(f => fs.existsSync(f))
+    .map(f => fs.readFileSync(f, 'utf-8'))
+    .join('\n\n');
+
+  return validateManuscript(combined, journalId);
+}