docrev 0.8.1 → 0.8.5

package/lib/journals.js

@@ -1,629 +0,0 @@
-/**
- * Journal validation profiles
- * Check manuscripts against journal-specific requirements
- */
-
-import * as fs from 'fs';
-import * as path from 'path';
-import { loadCustomProfiles } from './plugins.js';
-
-/**
- * Journal requirement profiles
- * Based on publicly available author guidelines
- */
-export const JOURNAL_PROFILES = {
-  nature: {
-    name: 'Nature',
-    url: 'https://www.nature.com/nature/for-authors',
-    requirements: {
-      wordLimit: { main: 3000, abstract: 150, title: 90 },
-      references: { max: 50, doiRequired: true },
-      figures: { max: 6, combinedWithTables: true },
-      sections: {
-        required: ['Abstract', 'Introduction', 'Results', 'Discussion', 'Methods'],
-        methodsPosition: 'end',
-      },
-      authors: { maxInitial: null, correspondingRequired: true },
-    },
-  },
-
-  science: {
-    name: 'Science',
-    url: 'https://www.science.org/content/page/instructions-preparing-initial-manuscript',
-    requirements: {
-      wordLimit: { main: 2500, abstract: 125, title: 120 },
-      references: { max: 40, doiRequired: true },
-      figures: { max: 4, combinedWithTables: true },
-      sections: {
-        required: ['Abstract', 'Introduction', 'Results', 'Discussion'],
-        supplementary: true,
-      },
-      authors: { maxInitial: null, correspondingRequired: true },
-    },
-  },
-
-  'plos-one': {
-    name: 'PLOS ONE',
-    url: 'https://journals.plos.org/plosone/s/submission-guidelines',
-    requirements: {
-      wordLimit: { main: null, abstract: 300, title: 250 },
-      references: { max: null, doiRequired: false },
-      figures: { max: null, combinedWithTables: false },
-      sections: {
-        required: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
-        methodsPosition: 'before-results',
-      },
-      authors: { maxInitial: null, correspondingRequired: true },
-      dataAvailability: true,
-    },
-  },
-
-  'pnas': {
-    name: 'PNAS',
-    url: 'https://www.pnas.org/author-center/submitting-your-manuscript',
-    requirements: {
-      wordLimit: { main: 4500, abstract: 250, title: null },
-      references: { max: 50, doiRequired: true },
-      figures: { max: 6, combinedWithTables: true },
-      sections: {
-        required: ['Abstract', 'Introduction', 'Results', 'Discussion'],
-        significanceStatement: true,
-      },
-      authors: { maxInitial: null, correspondingRequired: true },
-    },
-  },
-
-  'ecology-letters': {
-    name: 'Ecology Letters',
-    url: 'https://onlinelibrary.wiley.com/page/journal/14610248/homepage/forauthors.html',
-    requirements: {
-      wordLimit: { main: 5000, abstract: 150, title: null },
-      references: { max: 50, doiRequired: true },
-      figures: { max: 6, combinedWithTables: true },
-      sections: {
-        required: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
-      },
-      authors: { maxInitial: null, correspondingRequired: true },
-      keywords: { min: 3, max: 10 },
-    },
-  },
-
-  'ecological-applications': {
-    name: 'Ecological Applications',
-    url: 'https://esajournals.onlinelibrary.wiley.com/hub/journal/19395582/author-guidelines',
-    requirements: {
-      wordLimit: { main: 7000, abstract: 350, title: null },
-      references: { max: null, doiRequired: true },
-      figures: { max: null, combinedWithTables: false },
-      sections: {
-        required: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
-      },
-      dataAvailability: true,
-    },
-  },
-
-  'molecular-ecology': {
-    name: 'Molecular Ecology',
-    url: 'https://onlinelibrary.wiley.com/page/journal/1365294x/homepage/forauthors.html',
-    requirements: {
-      wordLimit: { main: 8000, abstract: 250, title: null },
-      references: { max: null, doiRequired: true },
-      figures: { max: 8, combinedWithTables: false },
-      sections: {
-        required: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
-      },
-      dataAvailability: true,
-      keywords: { min: 4, max: 8 },
-    },
-  },
-
-  'elife': {
-    name: 'eLife',
-    url: 'https://reviewer.elifesciences.org/author-guide/full',
-    requirements: {
-      wordLimit: { main: null, abstract: 150, title: null },
-      references: { max: null, doiRequired: true },
-      figures: { max: null, combinedWithTables: false },
-      sections: {
-        required: ['Abstract', 'Introduction', 'Results', 'Discussion', 'Methods'],
-        methodsPosition: 'end',
-      },
-      impactStatement: true,
-    },
-  },
-
-  'cell': {
-    name: 'Cell',
-    url: 'https://www.cell.com/cell/authors',
-    requirements: {
-      wordLimit: { main: 7000, abstract: 150, title: null },
-      references: { max: 100, doiRequired: true },
-      figures: { max: 7, combinedWithTables: true },
-      sections: {
-        required: ['Abstract', 'Introduction', 'Results', 'Discussion'],
-        graphicalAbstract: true,
-        highlights: true,
-      },
-      authors: { maxInitial: null, correspondingRequired: true },
-    },
-  },
-
-  'current-biology': {
-    name: 'Current Biology',
-    url: 'https://www.cell.com/current-biology/authors',
-    requirements: {
-      wordLimit: { main: 5000, abstract: 150, title: 150 },
-      references: { max: 60, doiRequired: true },
-      figures: { max: 4, combinedWithTables: true },
-      sections: {
-        required: ['Summary', 'Results', 'Discussion'],
-      },
-      authors: { maxInitial: null, correspondingRequired: true },
-    },
-  },
-
-  'conservation-biology': {
-    name: 'Conservation Biology',
-    url: 'https://conbio.onlinelibrary.wiley.com/hub/journal/15231739/homepage/forauthors.html',
-    requirements: {
-      wordLimit: { main: 7000, abstract: 300, title: null },
-      references: { max: null, doiRequired: true },
-      figures: { max: 6, combinedWithTables: true },
-      sections: {
-        required: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
-      },
-      keywords: { min: 5, max: 10 },
-    },
-  },
-
-  'biological-conservation': {
-    name: 'Biological Conservation',
-    url: 'https://www.elsevier.com/journals/biological-conservation/0006-3207/guide-for-authors',
-    requirements: {
-      wordLimit: { main: 8000, abstract: 400, title: null },
-      references: { max: null, doiRequired: true },
-      figures: { max: null, combinedWithTables: false },
-      sections: {
-        required: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
-      },
-      highlights: true,
-      keywords: { min: 4, max: 6 },
-    },
-  },
-
-  'journal-of-ecology': {
-    name: 'Journal of Ecology',
-    url: 'https://besjournals.onlinelibrary.wiley.com/hub/journal/13652745/author-guidelines',
-    requirements: {
-      wordLimit: { main: 7000, abstract: 350, title: null },
-      references: { max: null, doiRequired: true },
-      figures: { max: null, combinedWithTables: false },
-      sections: {
-        required: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
-      },
-      keywords: { min: 4, max: 8 },
-    },
-  },
-
-  'functional-ecology': {
-    name: 'Functional Ecology',
-    url: 'https://besjournals.onlinelibrary.wiley.com/hub/journal/13652435/author-guidelines',
-    requirements: {
-      wordLimit: { main: 7000, abstract: 350, title: null },
-      references: { max: null, doiRequired: true },
-      figures: { max: null, combinedWithTables: false },
-      sections: {
-        required: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
-      },
-      keywords: { min: 4, max: 8 },
-    },
-  },
-
-  'global-change-biology': {
-    name: 'Global Change Biology',
-    url: 'https://onlinelibrary.wiley.com/page/journal/13652486/homepage/forauthors.html',
-    requirements: {
-      wordLimit: { main: 7000, abstract: 300, title: null },
-      references: { max: null, doiRequired: true },
-      figures: { max: 8, combinedWithTables: false },
-      sections: {
-        required: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
-      },
-      keywords: { min: 4, max: 8 },
-    },
-  },
-
-  'oikos': {
-    name: 'Oikos',
-    url: 'https://nsojournals.onlinelibrary.wiley.com/hub/journal/16000706/author-guidelines',
-    requirements: {
-      wordLimit: { main: 8000, abstract: 350, title: null },
-      references: { max: null, doiRequired: true },
-      figures: { max: null, combinedWithTables: false },
-      sections: {
-        required: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
-      },
-      keywords: { min: 4, max: 10 },
-    },
-  },
-
-  'oecologia': {
-    name: 'Oecologia',
-    url: 'https://www.springer.com/journal/442/submission-guidelines',
-    requirements: {
-      wordLimit: { main: 8000, abstract: 250, title: null },
-      references: { max: null, doiRequired: true },
-      figures: { max: null, combinedWithTables: false },
-      sections: {
-        required: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
-      },
-      keywords: { min: 4, max: 6 },
-    },
-  },
-
-  'biological-invasions': {
-    name: 'Biological Invasions',
-    url: 'https://www.springer.com/journal/10530/submission-guidelines',
-    requirements: {
-      wordLimit: { main: null, abstract: 250, title: null },
-      references: { max: null, doiRequired: true },
-      figures: { max: null, combinedWithTables: false },
-      sections: {
-        required: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
-      },
-      keywords: { min: 4, max: 6 },
-    },
-  },
-
-  'diversity-distributions': {
-    name: 'Diversity and Distributions',
-    url: 'https://onlinelibrary.wiley.com/page/journal/14724642/homepage/forauthors.html',
-    requirements: {
-      wordLimit: { main: 6000, abstract: 300, title: null },
-      references: { max: null, doiRequired: true },
-      figures: { max: 6, combinedWithTables: true },
-      sections: {
-        required: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
-      },
-      keywords: { min: 4, max: 8 },
-      biosketch: true,
-    },
-  },
-
-  'neobiota': {
-    name: 'NeoBiota',
-    url: 'https://neobiota.pensoft.net/about#Author_Guidelines',
-    requirements: {
-      wordLimit: { main: null, abstract: 350, title: null },
-      references: { max: null, doiRequired: true },
-      figures: { max: null, combinedWithTables: false },
-      sections: {
-        required: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
-      },
-      keywords: { min: 6, max: 12 },
-    },
-  },
-
-  'peerj': {
-    name: 'PeerJ',
-    url: 'https://peerj.com/about/author-instructions/',
-    requirements: {
-      wordLimit: { main: null, abstract: 500, title: null },
-      references: { max: null, doiRequired: false },
-      figures: { max: null, combinedWithTables: false },
-      sections: {
-        required: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
-      },
-    },
-  },
-};
-
-/**
- * Get all profiles (built-in + custom)
- * Custom profiles override built-in ones with the same ID
- * @returns {Object<string, Object>}
- */
-function getAllProfiles() {
-  const customProfiles = loadCustomProfiles();
-  return { ...JOURNAL_PROFILES, ...customProfiles };
-}
-
-/**
- * List all available journal profiles
- * @param {object} options
- * @param {boolean} options.includeCustom - Include custom profiles (default: true)
- * @param {boolean} options.customOnly - Only show custom profiles
- * @returns {Array<{id: string, name: string, url: string, custom?: boolean}>}
- */
-export function listJournals(options = {}) {
-  const { includeCustom = true, customOnly = false } = options;
-
-  const profiles = customOnly
-    ? loadCustomProfiles()
-    : includeCustom
-      ? getAllProfiles()
-      : JOURNAL_PROFILES;
-
-  return Object.entries(profiles).map(([id, profile]) => ({
-    id,
-    name: profile.name,
-    url: profile.url,
-    custom: profile.custom || false,
-  }));
-}
-
-/**
- * Get a specific journal profile
- * @param {string} journalId
- * @returns {Object|null}
- */
-export function getJournalProfile(journalId) {
-  const normalized = journalId.toLowerCase().replace(/\s+/g, '-');
-  const profiles = getAllProfiles();
-  return profiles[normalized] || null;
-}
-
-/**
- * Count words in text (excluding markdown syntax)
- * @param {string} text
- * @returns {number}
- */
-function countWords(text) {
-  // Remove markdown syntax
-  let clean = text
-    .replace(/^---[\s\S]*?---/m, '') // YAML frontmatter
-    .replace(/!\[.*?\]\(.*?\)/g, '') // Images
-    .replace(/\[([^\]]+)\]\([^)]+\)/g, '$1') // Links
-    .replace(/#+\s*/g, '') // Headers
-    .replace(/\*\*|__/g, '') // Bold
-    .replace(/\*|_/g, '') // Italic
-    .replace(/`[^`]+`/g, '') // Inline code
-    .replace(/```[\s\S]*?```/g, '') // Code blocks
-    .replace(/\{[^}]+\}/g, '') // CriticMarkup and attributes
-    .replace(/@\w+:\w+/g, '') // Cross-references
-    .replace(/@\w+/g, '') // Citations
-    .replace(/\|[^|]+\|/g, ' ') // Table cells
-    .replace(/[-=]{3,}/g, '') // Horizontal rules
-    .replace(/\n+/g, ' ') // Newlines
-    .replace(/\s+/g, ' ') // Multiple spaces
-    .trim();
-
-  return clean.split(/\s+/).filter(w => w.length > 0).length;
-}
-
-/**
- * Extract abstract from markdown
- * @param {string} text
- * @returns {string|null}
- */
-function extractAbstract(text) {
-  // Try to find abstract section
-  const patterns = [
-    /^#+\s*Abstract\s*\n([\s\S]*?)(?=^#+|\Z)/mi,
-    /^Abstract[:\s]*\n([\s\S]*?)(?=^#+|\n\n)/mi,
-  ];
-
-  for (const pattern of patterns) {
-    const match = text.match(pattern);
-    if (match) {
-      return match[1].trim();
-    }
-  }
-
-  return null;
-}
-
-/**
- * Extract title from markdown
- * @param {string} text
- * @returns {string|null}
- */
-function extractTitle(text) {
-  // Try YAML frontmatter
-  const yamlMatch = text.match(/^---\n[\s\S]*?title:\s*["']?([^"'\n]+)["']?[\s\S]*?\n---/m);
-  if (yamlMatch) {
-    return yamlMatch[1].trim();
-  }
-
-  // Try first H1
-  const h1Match = text.match(/^#\s+(.+)$/m);
-  if (h1Match) {
-    return h1Match[1].trim();
-  }
-
-  return null;
-}
-
-/**
- * Extract sections from markdown
- * @param {string} text
- * @returns {string[]}
- */
-function extractSections(text) {
-  const sections = [];
-  const headerPattern = /^#+\s+(.+)$/gm;
-  let match;
-
-  while ((match = headerPattern.exec(text)) !== null) {
-    sections.push(match[1].trim());
-  }
-
-  return sections;
-}
-
-/**
- * Count figures in markdown
- * @param {string} text
- * @returns {number}
- */
-function countFigures(text) {
-  // Count images with figure captions
-  const figurePattern = /!\[.*?\]\(.*?\)(\{#fig:[^}]+\})?/g;
-  const matches = text.match(figurePattern) || [];
-  return matches.length;
-}
-
-/**
- * Count tables in markdown
- * @param {string} text
- * @returns {number}
- */
-function countTables(text) {
-  // 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
- * @param {string} text
- * @returns {number}
- */
-function countReferences(text) {
-  // Count unique citation keys
-  const citationPattern = /@(\w+)/g;
-  const citations = new Set();
-  let match;
-
-  while ((match = citationPattern.exec(text)) !== null) {
-    // Exclude cross-refs like @fig:label
-    if (!match[0].includes(':')) {
-      citations.add(match[1]);
-    }
-  }
-
-  return citations.size;
-}
-
-/**
- * Validate manuscript against journal requirements
- * @param {string} text - Markdown content
- * @param {string} journalId - Journal profile ID
- * @returns {{valid: boolean, errors: string[], warnings: string[], stats: Object}}
- */
-export function validateManuscript(text, journalId) {
-  const profile = getJournalProfile(journalId);
-
-  if (!profile) {
-    return {
-      valid: false,
-      errors: [`Unknown journal: ${journalId}`],
-      warnings: [],
-      stats: null,
-    };
-  }
-
-  const req = profile.requirements;
-  const errors = [];
-  const warnings = [];
-
-  // 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 = {
-    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})`);
-      }
-    }
-    if (req.wordLimit.title && title) {
-      if (title.length > req.wordLimit.title) {
-        warnings.push(`Title exceeds ${req.wordLimit.title} characters (current: ${title.length})`);
-      }
-    }
-  }
-
-  // References
-  if (req.references) {
-    if (req.references.max && refCount > req.references.max) {
-      errors.push(`References exceed ${req.references.max} (current: ${refCount})`);
-    }
-    if (req.references.doiRequired) {
-      warnings.push('DOI required for all references - run "rev doi check" to verify');
-    }
-  }
-
-  // Figures/tables
-  if (req.figures) {
-    const totalVisual = req.figures.combinedWithTables
-      ? figureCount + tableCount
-      : figureCount;
-    const label = req.figures.combinedWithTables ? 'figures + tables' : 'figures';
-
-    if (req.figures.max && totalVisual > req.figures.max) {
-      errors.push(`${label} exceed ${req.figures.max} (current: ${totalVisual})`);
-    }
-  }
-
-  // Required sections
-  if (req.sections?.required) {
-    for (const reqSection of req.sections.required) {
-      const found = sections.some(s =>
-        s.toLowerCase().includes(reqSection.toLowerCase())
-      );
-      if (!found) {
-        warnings.push(`Missing required section: ${reqSection}`);
-      }
-    }
-  }
-
-  // Data availability
-  if (req.dataAvailability) {
-    const hasDataStatement = sections.some(s =>
-      s.toLowerCase().includes('data') ||
-      text.toLowerCase().includes('data availability') ||
-      text.toLowerCase().includes('data statement')
-    );
-    if (!hasDataStatement) {
-      warnings.push('Data availability statement may be required');
-    }
-  }
-
-  return {
-    valid: errors.length === 0,
-    errors,
-    warnings,
-    stats,
-    journal: profile.name,
-    url: profile.url,
-  };
-}
-
-/**
- * Validate multiple files against journal requirements
- * @param {string[]} files - Markdown file paths
- * @param {string} journalId - Journal profile ID
- * @returns {Object}
- */
-export function validateProject(files, journalId) {
-  // 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);
-}