docrev 0.9.4 → 0.9.6

package/lib/diff-engine.ts

@@ -0,0 +1,465 @@
+/**
+ * Diff engine - diffing and annotation processing for Word→Markdown import
+ */
+
+import { diffWords, Change } from 'diff';
+import {
+  extractMarkdownPrefix,
+  protectAnchors,
+  restoreAnchors,
+  protectCrossrefs,
+  restoreCrossrefs,
+  protectMath,
+  restoreMath,
+  replaceRenderedMath,
+  protectCitations,
+  restoreCitations,
+  replaceRenderedCitations,
+  protectImages,
+  restoreImages,
+  matchWordImagesToOriginal,
+  protectTables,
+  restoreTables,
+} from './protect-restore.js';
+import { normalizeWhitespace } from './utils.js';
+import type { WordTable } from './word-extraction.js';
+
+// ============================================
+// Type Definitions
+// ============================================
+
+export interface GenerateSmartDiffOptions {
+  wordTables?: WordTable[];
+  imageRegistry?: any;
+}
+
+// ============================================
+// Functions
+// ============================================
+
+/**
+ * Fix citation and math annotations by preserving original markdown syntax
+ */
+export function fixCitationAnnotations(text: string, originalMd: string): string {
+  // Fix math annotations - preserve inline and display math
+  text = text.replace(/\{--(\$[^$]+\$)--\}/g, '$1');
+  text = text.replace(/\{--(\$\$[^$]+\$\$)--\}/g, '$1');
+
+  text = text.replace(/\{~~(\$[^$]+\$)~>[^~]+~~\}/g, '$1');
+  text = text.replace(/\{~~(\$\$[^$]+\$\$)~>[^~]+~~\}/g, '$1');
+
+  // Extract all citations from original markdown
+  const citationPattern = /\[@[^\]]+\]/g;
+  const originalCitations = [...originalMd.matchAll(citationPattern)].map(m => m[0]);
+
+  // Fix substitutions where left side has markdown citation
+  text = text.replace(/\{~~(\[@[^\]]+\])~>[^~]+~~\}/g, '$1');
+
+  // Fix substitutions where left side STARTS with markdown citation
+  text = text.replace(/\{~~(\[@[^\]]+\])\s*([^~]*)~>([^~]*)~~\}/g, (match, cite, oldText, newText) => {
+    if (oldText.trim() === '' && newText.trim() === '') {
+      return cite;
+    }
+    if (oldText.trim() || newText.trim()) {
+      return cite + (oldText.trim() !== newText.trim() ? ` {~~${oldText.trim()}~>${newText.trim()}~~}` : ` ${newText}`);
+    }
+    return cite;
+  });
+
+  // Fix deletions of markdown citations
+  text = text.replace(/\{--(\[@[^\]]+\])--\}/g, '$1');
+
+  // Fix insertions of rendered citations
+  text = text.replace(/\{\+\+\([A-Z][^)]*\d{4}[^)]*\)\+\+\}/g, '');
+
+  // Clean up broken multi-part substitutions
+  text = text.replace(/\{~~(@[A-Za-z]+\d{4})~>[^~]+~~\}/g, '[$1]');
+
+  // Fix citations split across substitution boundaries
+  text = text.replace(/\{~~\[@~>[^~]*~~\}([A-Za-z]+\d{4})\]/g, '[@$1]');
+
+  // Clean up any remaining partial citations
+  text = text.replace(/\{~~;\s*@([A-Za-z]+\d{4})\]~>[^~]*~~\}/g, '; [@$1]');
+
+  // Remove rendered citation insertions (with Unicode support)
+  text = text.replace(/\{\+\+\(\p{Lu}\p{L}*(?:\s+et\s+al\.?)?\s+\d{4}[a-z]?(?:[;,]\s*\p{Lu}\p{L}*(?:\s+et\s+al\.?)?\s+\d{4}[a-z]?)*\)\+\+\}/gu, '');
+  text = text.replace(/\{\+\+\(\p{Lu}\p{L}*(?:\s+et\s+al\.?)?\s+\d{4}[a-z]?(?:[;,]\s*\p{Lu}\p{L}*(?:\s+et\s+al\.?)?\s+\d{4}[a-z]?)*\)\.\s*\+\+\}/gu, '');
+
+  // Trailing citation fragments
+  text = text.replace(/\{\+\+\d{4}[a-z]?(?:[;,]\s*(?:\p{Lu}\p{L}*(?:\s+et\s+al\.?)?\s+)?\d{4}[a-z]?)*\)\.\s*\+\+\}/gu, '');
+  text = text.replace(/\{\+\+\d{4}[a-z]?(?:[;,]\s*(?:\p{Lu}\p{L}*(?:\s+et\s+al\.?)?\s+)?\d{4}[a-z]?)*\)\s*\+\+\}/gu, '');
+
+  // Just year with closing paren
+  text = text.replace(/\{\+\+\d{4}[a-z]?\)\.\s*\+\+\}/g, '');
+  text = text.replace(/\{\+\+\d{4}[a-z]?\)\s*\+\+\}/g, '');
+
+  // Leading citation fragments
+  text = text.replace(/\{\+\+\(?\p{Lu}\p{L}*(?:\s+et\s+al\.?)?\s*\+\+\}/gu, '');
+
+  // Semicolon-separated fragments
+  text = text.replace(/\{\+\+[;,]\s*\p{Lu}\p{L}*(?:\s+et\s+al\.?)?\s+\d{4}[a-z]?\+\+\}/gu, '');
+
+  // Year ranges with authors
+  text = text.replace(/\{\+\+\p{Lu}\p{L}*(?:\s+et\s+al\.?)?\s+\d{4}[a-z]?(?:[;,]\s*\p{Lu}\p{L}*(?:\s+et\s+al\.?)?\s+\d{4}[a-z]?)*\)\s*\+\+\}/gu, '');
+  text = text.replace(/\{\+\+\p{Lu}\p{L}*(?:\s+et\s+al\.?)?\s+\d{4}[a-z]?(?:[;,]\s*\p{Lu}\p{L}*(?:\s+et\s+al\.?)?\s+\d{4}[a-z]?)*\)\.\s*\+\+\}/gu, '');
+
+  // Clean up double spaces and orphaned punctuation
+  text = text.replace(/  +/g, ' ');
+  text = text.replace(/\s+\./g, '.');
+  text = text.replace(/\s+,/g, ',');
+
+  // Final cleanup - remove empty annotations
+  text = text.replace(/\{~~\s*~>\s*~~\}/g, '');
+  text = text.replace(/\{\+\+\s*\+\+\}/g, '');
+  text = text.replace(/\{--\s*--\}/g, '');
+
+  return text;
+}
+
+/**
+ * Strip markdown syntax to get plain text
+ */
+function stripMarkdownSyntax(md: string): string {
+  return md
+    .replace(/^---[\s\S]*?---\n*/m, '')
+    .replace(/^#{1,6}\s+/gm, '')
+    .replace(/(\*\*|__)(.*?)\1/g, '$2')
+    .replace(/(\*|_)(.*?)\1/g, '$2')
+    .replace(/\[([^\]]+)\]\([^)]+\)/g, '$1')
+    .replace(/!\[([^\]]*)\]\([^)]+\)/g, '')
+    .replace(/`([^`]+)`/g, '$1')
+    .replace(/```[\s\S]*?```/g, '')
+    .replace(/^>\s*/gm, '')
+    .replace(/^[-*_]{3,}\s*$/gm, '')
+    .replace(/^[\s]*[-*+]\s+/gm, '')
+    .replace(/^[\s]*\d+\.\s+/gm, '')
+    .replace(/\|/g, ' ')
+    .replace(/^[-:]+$/gm, '')
+    .replace(/\n{3,}/g, '\n\n')
+    .trim();
+}
+
+/**
+ * Inject Word tables (extracted from XML) into pandoc text output
+ */
+function injectWordTables(pandocText: string, wordTables: WordTable[]): string {
+  if (!wordTables || wordTables.length === 0) {
+    return pandocText;
+  }
+
+  let result = pandocText;
+
+  for (const table of wordTables) {
+    const firstLine = table.markdown.split('\n')[0];
+    const headerCells = firstLine
+      .split('|')
+      .map((c) => c.trim())
+      .filter((c) => c.length > 0);
+
+    if (headerCells.length === 0) continue;
+
+    const firstCell = headerCells[0];
+    const startIdx = result.indexOf(firstCell);
+
+    if (startIdx === -1) continue;
+
+    const lastLine = table.markdown.split('\n').pop();
+    const lastCells = lastLine!
+      .split('|')
+      .map((c) => c.trim())
+      .filter((c) => c.length > 0);
+    const lastCell = lastCells[lastCells.length - 1] || lastCells[0];
+
+    const endIdx = result.indexOf(lastCell, startIdx);
+    if (endIdx === -1) continue;
+
+    let regionStart = result.lastIndexOf('\n\n', startIdx);
+    if (regionStart === -1) regionStart = 0;
+    else regionStart += 2;
+
+    let regionEnd = result.indexOf('\n\n', endIdx + lastCell.length);
+    if (regionEnd === -1) regionEnd = result.length;
+
+    result = result.slice(0, regionStart) + table.markdown + '\n\n' + result.slice(regionEnd);
+  }
+
+  return result;
+}
+
+/**
+ * Generate annotated markdown by diffing original MD against Word text
+ */
+export function generateAnnotatedDiff(originalMd: string, wordText: string, author: string = 'Reviewer'): string {
+  const normalizedOriginal = normalizeWhitespace(originalMd);
+  const normalizedWord = normalizeWhitespace(wordText);
+
+  const changes = diffWords(normalizedOriginal, normalizedWord);
+
+  let result = '';
+
+  for (const part of changes) {
+    if (part.added) {
+      result += `{++${part.value}++}`;
+    } else if (part.removed) {
+      result += `{--${part.value}--}`;
+    } else {
+      result += part.value;
+    }
+  }
+
+  return result;
+}
+
+/**
+ * Smart paragraph-level diff that preserves markdown structure
+ */
+export function generateSmartDiff(
+  originalMd: string,
+  wordText: string,
+  author: string = 'Reviewer',
+  options: GenerateSmartDiffOptions = {}
+): string {
+  const { wordTables = [], imageRegistry = null } = options;
+
+  // Inject Word tables into pandoc output
+  let wordTextWithTables = injectWordTables(wordText, wordTables);
+
+  // Protect markdown tables
+  const { text: mdWithTablesProtected, tables } = protectTables(originalMd);
+
+  // Also protect tables in Word text
+  const { text: wordWithTablesProtected, tables: wordTableBlocks } = protectTables(wordTextWithTables);
+
+  // Protect images
+  const { text: mdWithImagesProtected, images: origImages } = protectImages(mdWithTablesProtected, imageRegistry);
+
+  const { text: wordWithImagesProtected, images: wordImages } = protectImages(wordWithTablesProtected, imageRegistry);
+
+  // Match Word images to original images
+  const imageMapping = matchWordImagesToOriginal(origImages, wordImages, imageRegistry);
+
+  // Replace Word image placeholders with matching original placeholders
+  let wordWithMappedImages = wordWithImagesProtected;
+  for (const [wordPlaceholder, origPlaceholder] of imageMapping) {
+    wordWithMappedImages = wordWithMappedImages.split(wordPlaceholder).join(origPlaceholder);
+  }
+
+  // Protect figure/table anchors
+  const { text: mdWithAnchorsProtected, anchors: figAnchors } = protectAnchors(mdWithImagesProtected);
+
+  // Protect cross-references
+  const { text: mdWithXrefsProtected, crossrefs } = protectCrossrefs(mdWithAnchorsProtected);
+
+  // Protect math
+  const { text: mdWithMathProtected, mathBlocks } = protectMath(mdWithXrefsProtected);
+
+  // Protect citations
+  const { text: mdProtected, citations } = protectCitations(mdWithMathProtected);
+
+  // Replace rendered elements in Word text
+  let wordProtected = wordWithMappedImages;
+  wordProtected = replaceRenderedMath(wordProtected, mathBlocks);
+  wordProtected = replaceRenderedCitations(wordProtected, citations.length);
+
+  // Split into paragraphs
+  const originalParas = mdProtected.split(/\n\n+/);
+  const wordParas = wordProtected.split(/\n\n+/);
+
+  const result: string[] = [];
+
+  // Try to match paragraphs intelligently
+  let wordIdx = 0;
+
+  for (let i = 0; i < originalParas.length; i++) {
+    const orig = originalParas[i] || '';
+    const { prefix: mdPrefix, content: origContent } = extractMarkdownPrefix(orig.split('\n')[0]);
+
+    // Find best matching word paragraph
+    let bestMatch = -1;
+    let bestScore = 0;
+
+    for (let j = wordIdx; j < Math.min(wordIdx + 3, wordParas.length); j++) {
+      const wordPara = wordParas[j] || '';
+      const origWords = new Set(origContent.toLowerCase().split(/\s+/));
+      const wordWords = wordPara.toLowerCase().split(/\s+/);
+      const common = wordWords.filter((w) => origWords.has(w)).length;
+      const score = common / Math.max(origWords.size, wordWords.length);
+
+      if (score > bestScore && score > 0.3) {
+        bestScore = score;
+        bestMatch = j;
+      }
+    }
+
+    if (bestMatch === -1) {
+      if (mdPrefix && wordIdx < wordParas.length) {
+        const wordPara = wordParas[wordIdx];
+        if (wordPara.toLowerCase().includes(origContent.toLowerCase().slice(0, 20))) {
+          bestMatch = wordIdx;
+        }
+      }
+    }
+
+    if (bestMatch >= 0) {
+      const word = wordParas[bestMatch];
+
+      const origStripped = stripMarkdownSyntax(orig);
+      const wordNormalized = normalizeWhitespace(word);
+
+      if (origStripped === wordNormalized) {
+        result.push(orig);
+      } else {
+        const changes = diffWords(origStripped, wordNormalized);
+        let annotated = mdPrefix;
+
+        for (const part of changes) {
+          if (part.added) {
+            annotated += `{++${part.value}++}`;
+          } else if (part.removed) {
+            annotated += `{--${part.value}--}`;
+          } else {
+            annotated += part.value;
+          }
+        }
+
+        result.push(annotated);
+      }
+
+      wordIdx = bestMatch + 1;
+    } else {
+      // Paragraph deleted entirely
+      if (mdPrefix && mdPrefix.match(/^#{1,6}\s+/)) {
+        result.push(orig);
+      } else {
+        result.push(`{--${orig}--}`);
+      }
+    }
+  }
+
+  // Any remaining word paragraphs are additions
+  for (let j = wordIdx; j < wordParas.length; j++) {
+    const word = wordParas[j];
+    if (word.trim()) {
+      result.push(`{++${word}++}`);
+    }
+  }
+
+  // Restore protected content
+  let finalResult = result.join('\n\n');
+  finalResult = restoreCitations(finalResult, citations);
+  finalResult = restoreMath(finalResult, mathBlocks);
+  finalResult = restoreCrossrefs(finalResult, crossrefs);
+  finalResult = restoreAnchors(finalResult, figAnchors);
+  finalResult = restoreImages(finalResult, origImages);
+  finalResult = restoreImages(finalResult, wordImages);
+  finalResult = restoreTables(finalResult, tables);
+  finalResult = restoreTables(finalResult, wordTableBlocks);
+
+  return finalResult;
+}
+
+/**
+ * Clean up redundant adjacent annotations
+ */
+export function cleanupAnnotations(text: string): string {
+  // Convert adjacent delete+insert to substitution
+  text = text.replace(/\{--(.+?)--\}\s*\{\+\+(.+?)\+\+\}/g, '{~~$1~>$2~~}');
+
+  // Also handle insert+delete
+  text = text.replace(/\{\+\+(.+?)\+\+\}\s*\{--(.+?)--\}/g, '{~~$2~>$1~~}');
+
+  // Fix malformed patterns
+  text = text.replace(/\{--([^}]+?)~>([^}]+?)~~\}/g, '{~~$1~>$2~~}');
+
+  // Fix malformed substitutions that got split
+  text = text.replace(/\{~~([^~]+)\s*--\}/g, '{--$1--}');
+  text = text.replace(/\{\+\+([^+]+)~~\}/g, '{++$1++}');
+
+  // Clean up empty annotations
+  text = text.replace(/\{--\s*--\}/g, '');
+  text = text.replace(/\{\+\+\s*\+\+\}/g, '');
+
+  // Clean up double spaces in prose, but preserve table formatting
+  const lines = text.split('\n');
+  let inTable = false;
+
+  const processedLines = lines.map((line, idx) => {
+    const isSeparator = /^[-]+(\s+[-]+)+\s*$/.test(line.trim());
+
+    const looksLikeTableRow = /\S+\s{2,}\S+/.test(line);
+
+    if (isSeparator) {
+      if (!inTable) {
+        inTable = true;
+      }
+      return line;
+    }
+
+    if (inTable) {
+      if (line.trim() === '') {
+        let lookAhead = idx + 1;
+        let foundTableContent = false;
+        let foundEndSeparator = false;
+
+        while (lookAhead < lines.length && lookAhead < idx + 20) {
+          const nextLine = lines[lookAhead].trim();
+
+          if (nextLine === '') {
+            lookAhead++;
+            continue;
+          }
+
+          if (/^[-]+(\s+[-]+)+\s*$/.test(nextLine)) {
+            foundEndSeparator = true;
+            break;
+          }
+
+          if (/\S+\s{2,}\S+/.test(nextLine)) {
+            foundTableContent = true;
+            break;
+          }
+
+          if (/^\*[^*]+\*\s*$/.test(nextLine)) {
+            foundTableContent = true;
+            break;
+          }
+
+          if (lines[lookAhead].startsWith('  ')) {
+            lookAhead++;
+            continue;
+          }
+
+          break;
+        }
+
+        if (foundTableContent || foundEndSeparator) {
+          return line;
+        }
+
+        inTable = false;
+        return line;
+      }
+
+      return line;
+    }
+
+    if (looksLikeTableRow) {
+      let nextIdx = idx + 1;
+      while (nextIdx < lines.length && lines[nextIdx].trim() === '') {
+        nextIdx++;
+      }
+      if (nextIdx < lines.length && /^[-]+(\s+[-]+)+\s*$/.test(lines[nextIdx].trim())) {
+        return line;
+      }
+    }
+
+    if (line.trim().startsWith('|')) {
+      return line;
+    }
+
+    return line.replace(/  +/g, ' ');
+  });
+  text = processedLines.join('\n');
+
+  return text;
+}

package/lib/git.ts

@@ -103,14 +103,18 @@ export function getChangedFiles(fromRef: string, toRef: string = 'HEAD'): Change
 }
 
 /**
- * Get commit history for a file
- * @param filePath - Path to file
- * @param limit - Maximum number of commits to return
+ * Run git log with a given format and optional file path, parse pipe-delimited output
  */
-export function getFileHistory(filePath: string, limit: number = 10): CommitInfo[] {
+function runGitLog(
+  format: string,
+  limit: number,
+  fields: (keyof CommitInfo)[],
+  filePath?: string,
+): CommitInfo[] {
   try {
+    const fileArg = filePath ? ` -- "${filePath}"` : '';
     const output = execSync(
-      `git log --format="%h|%ci|%s" -n ${limit} -- "${filePath}"`,
+      `git log --format="${format}" -n ${limit}${fileArg}`,
       { stdio: 'pipe' }
     ).toString().trim();
 
@@ -118,18 +122,26 @@ export function getFileHistory(filePath: string, limit: number = 10): CommitInfo
 
     return output.split('\n').map(line => {
       const parts = line.split('|');
-      return {
-        hash: parts[0] ?? '',
-        date: parts[1] ?? '',
-        message: parts[2] ?? '',
-        author: ''
-      };
+      const entry: CommitInfo = { hash: '', date: '', author: '', message: '' };
+      for (let i = 0; i < fields.length; i++) {
+        entry[fields[i]] = parts[i] ?? '';
+      }
+      return entry;
     });
   } catch {
     return [];
   }
 }
 
+/**
+ * Get commit history for a file
+ * @param filePath - Path to file
+ * @param limit - Maximum number of commits to return
+ */
+export function getFileHistory(filePath: string, limit: number = 10): CommitInfo[] {
+  return runGitLog('%h|%ci|%s', limit, ['hash', 'date', 'message'], filePath);
+}
+
 /**
  * Compare file content between two refs
  * @param filePath - Path to file
@@ -194,26 +206,7 @@ export function getWordCountDiff(
  * @param limit - Maximum number of commits to return
  */
 export function getRecentCommits(limit: number = 10): CommitInfo[] {
-  try {
-    const output = execSync(
-      `git log --format="%h|%ci|%an|%s" -n ${limit}`,
-      { stdio: 'pipe' }
-    ).toString().trim();
-
-    if (!output) return [];
-
-    return output.split('\n').map(line => {
-      const parts = line.split('|');
-      return {
-        hash: parts[0] ?? '',
-        date: parts[1] ?? '',
-        author: parts[2] ?? '',
-        message: parts[3] ?? ''
-      };
-    });
-  } catch {
-    return [];
-  }
+  return runGitLog('%h|%ci|%an|%s', limit, ['hash', 'date', 'author', 'message']);
 }
 
 /**