docrev 0.11.2 → 0.12.0

package/lib/journals.ts

@@ -1,543 +0,0 @@
-/**
- * Journal validation profiles
- * Check manuscripts against journal-specific requirements
- */
-
-import * as fs from 'fs';
-import * as path from 'path';
-import type { JournalProfile, JournalRequirements, JournalFormatting, 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'],
-    },
-    formatting: {
-      csl: 'nature',
-      pdf: { fontsize: '11pt', geometry: 'margin=2.5cm', linestretch: 2 },
-    },
-  },
-
-  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'],
-    },
-    formatting: {
-      csl: 'science',
-      pdf: { fontsize: '12pt', geometry: 'margin=1in', linestretch: 2 },
-    },
-  },
-
-  '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'],
-    },
-    formatting: {
-      csl: 'plos',
-      pdf: { fontsize: '12pt', geometry: 'margin=1in', linestretch: 2 },
-    },
-  },
-
-  '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'],
-    },
-    formatting: {
-      csl: 'pnas',
-      pdf: { documentclass: 'article', fontsize: '9pt', geometry: 'margin=2cm', linestretch: 1.2, numbersections: false },
-    },
-  },
-
-  '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'],
-    },
-    formatting: {
-      csl: 'elife',
-      pdf: { fontsize: '11pt', geometry: 'margin=2.5cm', linestretch: 1.5 },
-    },
-  },
-
-  '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'],
-    },
-    formatting: {
-      csl: 'cell',
-      pdf: { fontsize: '12pt', geometry: 'margin=2.5cm', linestretch: 2 },
-    },
-  },
-
-  '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'],
-    },
-  },
-
-  'methods-ecology-evolution': {
-    name: 'Methods in Ecology and Evolution',
-    url: 'https://besjournals.onlinelibrary.wiley.com/hub/journal/2041210x/author-guidelines',
-    requirements: {
-      wordLimit: { main: 7000, abstract: 350 },
-      references: { doiRequired: true },
-      sections: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
-    },
-    formatting: {
-      csl: 'methods-in-ecology-and-evolution',
-      pdf: { fontsize: '12pt', geometry: 'margin=2.5cm', linestretch: 2 },
-    },
-  },
-};
-
-/**
- * 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);
-}