docrev 0.2.1 → 0.5.0

package/lib/journals.js

@@ -0,0 +1,605 @@
+/**
+ * Journal validation profiles
+ * Check manuscripts against journal-specific requirements
+ */
+
+import * as fs from 'fs';
+import * as path from 'path';
+
+/**
+ * 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'],
+      },
+    },
+  },
+};
+
+/**
+ * List all available journal profiles
+ * @returns {Array<{id: string, name: string, url: string}>}
+ */
+export function listJournals() {
+  return Object.entries(JOURNAL_PROFILES).map(([id, profile]) => ({
+    id,
+    name: profile.name,
+    url: profile.url,
+  }));
+}
+
+/**
+ * Get a specific journal profile
+ * @param {string} journalId
+ * @returns {Object|null}
+ */
+export function getJournalProfile(journalId) {
+  const normalized = journalId.toLowerCase().replace(/\s+/g, '-');
+  return JOURNAL_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);
+}