docrev 0.10.1 → 0.11.0

package/dist/lib/themes.js

@@ -556,23 +556,23 @@ export function generateBeamerColors(theme) {
     const bg = hexToRgb(colors.background);
     const bgDark = hexToRgb(colors.backgroundDark);
     const text = hexToRgb(colors.text);
-    return `
-% Theme: ${theme.displayName}
-% ${theme.description}
-\\definecolor{ThemePrimary}{RGB}{${primary.r},${primary.g},${primary.b}}
-\\definecolor{ThemeSecondary}{RGB}{${secondary.r},${secondary.g},${secondary.b}}
-\\definecolor{ThemeAccent}{RGB}{${accent.r},${accent.g},${accent.b}}
-\\definecolor{ThemeBackground}{RGB}{${bg.r},${bg.g},${bg.b}}
-\\definecolor{ThemeBackgroundDark}{RGB}{${bgDark.r},${bgDark.g},${bgDark.b}}
-\\definecolor{ThemeText}{RGB}{${text.r},${text.g},${text.b}}
-
-\\setbeamercolor{structure}{fg=ThemePrimary}
-\\setbeamercolor{frametitle}{fg=ThemePrimary,bg=ThemeBackground}
-\\setbeamercolor{title}{fg=ThemePrimary}
-\\setbeamercolor{subtitle}{fg=ThemeSecondary}
-\\setbeamercolor{normal text}{fg=ThemeText,bg=ThemeBackground}
-\\setbeamercolor{alerted text}{fg=ThemeAccent}
-\\setbeamercolor{example text}{fg=ThemeSecondary}
+    return `
+% Theme: ${theme.displayName}
+% ${theme.description}
+\\definecolor{ThemePrimary}{RGB}{${primary.r},${primary.g},${primary.b}}
+\\definecolor{ThemeSecondary}{RGB}{${secondary.r},${secondary.g},${secondary.b}}
+\\definecolor{ThemeAccent}{RGB}{${accent.r},${accent.g},${accent.b}}
+\\definecolor{ThemeBackground}{RGB}{${bg.r},${bg.g},${bg.b}}
+\\definecolor{ThemeBackgroundDark}{RGB}{${bgDark.r},${bgDark.g},${bgDark.b}}
+\\definecolor{ThemeText}{RGB}{${text.r},${text.g},${text.b}}
+
+\\setbeamercolor{structure}{fg=ThemePrimary}
+\\setbeamercolor{frametitle}{fg=ThemePrimary,bg=ThemeBackground}
+\\setbeamercolor{title}{fg=ThemePrimary}
+\\setbeamercolor{subtitle}{fg=ThemeSecondary}
+\\setbeamercolor{normal text}{fg=ThemeText,bg=ThemeBackground}
+\\setbeamercolor{alerted text}{fg=ThemeAccent}
+\\setbeamercolor{example text}{fg=ThemeSecondary}
 `.trim();
 }
 /**
@@ -580,40 +580,40 @@ export function generateBeamerColors(theme) {
  */
 export function generatePptxCSS(theme) {
     const { colors, fonts } = theme;
-    return `
-/* Theme: ${theme.displayName} */
-/* ${theme.description} */
-
-:root {
-  --theme-primary: ${colors.primary};
-  --theme-secondary: ${colors.secondary};
-  --theme-accent: ${colors.accent};
-  --theme-background: ${colors.background};
-  --theme-background-dark: ${colors.backgroundDark};
-  --theme-text: ${colors.text};
-  --theme-text-light: ${colors.textLight};
-
-  --font-heading: '${fonts.heading}', sans-serif;
-  --font-body: '${fonts.body}', sans-serif;
-  --font-mono: '${fonts.mono}', monospace;
-}
-
-/* Slide styles */
-.dark {
-  background-color: var(--theme-background-dark);
-  color: var(--theme-text-light);
-}
-
-.cover, .thanks, .section {
-  background-color: var(--theme-primary);
-  color: var(--theme-text-light);
-  text-align: center;
-}
-
-.accent {
-  background-color: var(--theme-accent);
-  color: var(--theme-text);
-}
+    return `
+/* Theme: ${theme.displayName} */
+/* ${theme.description} */
+
+:root {
+  --theme-primary: ${colors.primary};
+  --theme-secondary: ${colors.secondary};
+  --theme-accent: ${colors.accent};
+  --theme-background: ${colors.background};
+  --theme-background-dark: ${colors.backgroundDark};
+  --theme-text: ${colors.text};
+  --theme-text-light: ${colors.textLight};
+
+  --font-heading: '${fonts.heading}', sans-serif;
+  --font-body: '${fonts.body}', sans-serif;
+  --font-mono: '${fonts.mono}', monospace;
+}
+
+/* Slide styles */
+.dark {
+  background-color: var(--theme-background-dark);
+  color: var(--theme-text-light);
+}
+
+.cover, .thanks, .section {
+  background-color: var(--theme-primary);
+  color: var(--theme-text-light);
+  text-align: center;
+}
+
+.accent {
+  background-color: var(--theme-accent);
+  color: var(--theme-text);
+}
 `.trim();
 }
 /**

package/dist/lib/types.d.ts

@@ -188,7 +188,13 @@ export interface BibEntry {
 }
 export interface DoiCheckResult {
     valid: boolean;
-    source?: 'crossref' | 'datacite';
+    source?: 'crossref' | 'datacite' | 'doi.org';
+    /**
+     * True when the registry could not be reached (network error, timeout, or
+     * 5xx) — the DOI's validity is unknown, distinct from a definitive "not
+     * found". Callers must not report an unreachable DOI as invalid.
+     */
+    unreachable?: boolean;
     metadata?: {
         title: string;
         authors: string[];
@@ -229,6 +235,8 @@ export interface BibCheckResult {
     }>;
     valid: number;
     invalid: number;
+    /** DOIs whose registry could not be reached (network/timeout) — not invalid. */
+    unreachable: number;
     missing: number;
     skipped: number;
 }

package/dist/lib/types.d.ts.map

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package/dist/lib/word-extraction.d.ts.map

@@ -1 +1 @@
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package/dist/lib/word-extraction.js

@@ -5,6 +5,7 @@ import * as fs from 'fs';
 import * as path from 'path';
 import { exec } from 'child_process';
 import { promisify } from 'util';
+import { buildDocTextModel, buildCommentAnchorModel, extractComments, openDocx, readPartText } from './ooxml.js';
 const execAsync = promisify(exec);
 // ============================================
 // Functions
@@ -13,123 +14,18 @@ const execAsync = promisify(exec);
  * Extract comments directly from Word docx comments.xml
  */
 export async function extractWordComments(docxPath) {
-    const AdmZip = (await import('adm-zip')).default;
-    const { parseStringPromise } = await import('xml2js');
-    const comments = [];
-    // Validate file exists
     if (!fs.existsSync(docxPath)) {
         throw new Error(`File not found: ${docxPath}`);
     }
-    try {
-        let zip;
-        try {
-            zip = new AdmZip(docxPath);
-        }
-        catch (err) {
-            throw new Error(`Invalid Word document (not a valid .docx file): ${err.message}`);
-        }
-        const commentsEntry = zip.getEntry('word/comments.xml');
-        if (!commentsEntry) {
-            return comments;
-        }
-        let commentsXml;
-        try {
-            commentsXml = commentsEntry.getData().toString('utf8');
-        }
-        catch (err) {
-            throw new Error(`Failed to read comments from document: ${err.message}`);
-        }
-        const parsed = await parseStringPromise(commentsXml, { explicitArray: false });
-        const commentsRoot = parsed['w:comments'];
-        if (!commentsRoot || !commentsRoot['w:comment']) {
-            return comments;
-        }
-        // Ensure it's an array
-        const commentNodes = Array.isArray(commentsRoot['w:comment'])
-            ? commentsRoot['w:comment']
-            : [commentsRoot['w:comment']];
-        // Map every paraId that lives inside a comment back to that comment's id.
-        // Word's commentsExtended.xml expresses threading via w15:paraIdParent,
-        // which references the parent's first <w:p>. Replies use a secondary
-        // (often-empty) <w:p>, so each comment may contribute multiple paraIds.
-        const paraIdToCommentId = new Map();
-        for (const comment of commentNodes) {
-            const id = comment.$?.['w:id'] || '';
-            const author = comment.$?.['w:author'] || 'Unknown';
-            const date = comment.$?.['w:date'] || '';
-            // Extract text from nested w:p/w:r/w:t elements and record paraIds.
-            let text = '';
-            const extractText = (node) => {
-                if (!node)
-                    return;
-                if (typeof node === 'string') {
-                    text += node;
-                    return;
-                }
-                if (node['w:t']) {
-                    const t = node['w:t'];
-                    text += typeof t === 'string' ? t : (t._ || t);
-                }
-                if (node['w:r']) {
-                    const runs = Array.isArray(node['w:r']) ? node['w:r'] : [node['w:r']];
-                    runs.forEach(extractText);
-                }
-                if (node['w:p']) {
-                    const paras = Array.isArray(node['w:p']) ? node['w:p'] : [node['w:p']];
-                    for (const para of paras) {
-                        const paraId = para?.$?.['w14:paraId'];
-                        if (paraId && id)
-                            paraIdToCommentId.set(paraId, id);
-                        extractText(para);
-                    }
-                }
-            };
-            extractText(comment);
-            comments.push({ id, author, date: date.slice(0, 10), text: text.trim() });
-        }
-        // Resolve parent links from commentsExtended.xml. Missing entry just
-        // means the docx has no threading metadata (e.g. legacy/non-Word source).
-        const extendedEntry = zip.getEntry('word/commentsExtended.xml');
-        if (extendedEntry && paraIdToCommentId.size > 0) {
-            let extendedXml = '';
-            try {
-                extendedXml = extendedEntry.getData().toString('utf8');
-            }
-            catch {
-                // Unreadable threading metadata is non-fatal; skip parent linking.
-            }
-            if (extendedXml) {
-                const parentByCommentId = new Map();
-                const exPattern = /<w15:commentEx\b([^>]*?)\/>/g;
-                let m;
-                while ((m = exPattern.exec(extendedXml)) !== null) {
-                    const attrs = m[1] ?? '';
-                    const paraIdMatch = attrs.match(/w15:paraId="([^"]+)"/);
-                    const parentMatch = attrs.match(/w15:paraIdParent="([^"]+)"/);
-                    if (!paraIdMatch || !parentMatch)
-                        continue;
-                    const childCommentId = paraIdToCommentId.get(paraIdMatch[1]);
-                    const parentCommentId = paraIdToCommentId.get(parentMatch[1]);
-                    if (childCommentId && parentCommentId && childCommentId !== parentCommentId) {
-                        parentByCommentId.set(childCommentId, parentCommentId);
-                    }
-                }
-                for (const c of comments) {
-                    const parent = parentByCommentId.get(c.id);
-                    if (parent)
-                        c.parentId = parent;
-                }
-            }
-        }
-    }
-    catch (err) {
-        // Re-throw with more context if it's already an Error we created
-        if (err.message.includes('Invalid Word document') || err.message.includes('File not found')) {
-            throw err;
-        }
-        throw new Error(`Error extracting comments from ${path.basename(docxPath)}: ${err.message}`);
-    }
-    return comments;
+    const zip = openDocx(docxPath);
+    // Word truncates the stored date to its day for display; keep that contract.
+    return extractComments(zip).map((c) => ({
+        id: c.id,
+        author: c.author,
+        date: c.date.slice(0, 10),
+        text: c.text,
+        parentId: c.parentId,
+    }));
 }
 /**
  * Extract comment anchor texts from document.xml with surrounding context
@@ -137,141 +33,38 @@ export async function extractWordComments(docxPath) {
  * Also returns fullDocText for section boundary matching
  */
 export async function extractCommentAnchors(docxPath) {
-    const AdmZip = (await import('adm-zip')).default;
     const anchors = new Map();
-    let fullDocText = '';
-    try {
-        const zip = new AdmZip(docxPath);
-        const docEntry = zip.getEntry('word/document.xml');
-        if (!docEntry) {
-            return { anchors, fullDocText };
-        }
-        const docXml = docEntry.getData().toString('utf8');
-        // ========================================
-        // STEP 1: Build text position mapping
-        // ========================================
-        const textNodePattern = /<w:t[^>]*>([^<]*)<\/w:t>/g;
-        const textNodes = [];
-        let textPosition = 0;
-        let nodeMatch;
-        while ((nodeMatch = textNodePattern.exec(docXml)) !== null) {
-            const rawText = nodeMatch[1] ?? '';
-            const decodedText = decodeXmlEntities(rawText);
-            textNodes.push({
-                xmlStart: nodeMatch.index,
-                xmlEnd: nodeMatch.index + nodeMatch[0].length,
-                textStart: textPosition,
-                textEnd: textPosition + decodedText.length,
-                text: decodedText
-            });
-            textPosition += decodedText.length;
-        }
-        fullDocText = textNodes.map(n => n.text).join('');
-        // Helper: convert XML position to text position
-        function xmlPosToTextPos(xmlPos) {
-            for (let i = 0; i < textNodes.length; i++) {
-                const node = textNodes[i];
-                if (!node)
-                    continue;
-                if (xmlPos >= node.xmlStart && xmlPos < node.xmlEnd) {
-                    return node.textStart;
-                }
-                if (xmlPos < node.xmlStart) {
-                    return node.textStart;
-                }
-            }
-            const lastNode = textNodes[textNodes.length - 1];
-            return lastNode ? lastNode.textEnd : 0;
-        }
-        // Helper: extract context before a position
-        function getContextBefore(position, maxLength = 150) {
-            const beforeText = fullDocText.slice(Math.max(0, position - maxLength), position);
-            const sentenceStart = beforeText.search(/[.!?]\s+[A-Z][^.!?]*$/);
-            return sentenceStart >= 0
-                ? beforeText.slice(sentenceStart + 2).trim()
-                : beforeText.slice(-80).trim();
-        }
-        // Helper: extract context after a position
-        function getContextAfter(position, maxLength = 150) {
-            const afterText = fullDocText.slice(position, position + maxLength);
-            const sentenceEnd = afterText.search(/[.!?]\s/);
-            return sentenceEnd >= 0
-                ? afterText.slice(0, sentenceEnd + 1).trim()
-                : afterText.slice(0, 80).trim();
-        }
-        // ========================================
-        // STEP 2: Collect all start/end markers separately
-        // ========================================
-        const startPattern = /<w:commentRangeStart[^>]*w:id="(\d+)"[^>]*\/?>/g;
-        const endPattern = /<w:commentRangeEnd[^>]*w:id="(\d+)"[^>]*\/?>/g;
-        const starts = new Map(); // id -> position after start tag
-        const ends = new Map(); // id -> position before end tag
-        let match;
-        while ((match = startPattern.exec(docXml)) !== null) {
-            const id = match[1];
-            if (!starts.has(id)) {
-                starts.set(id, match.index + match[0].length);
-            }
-        }
-        while ((match = endPattern.exec(docXml)) !== null) {
-            const id = match[1];
-            if (!ends.has(id)) {
-                ends.set(id, match.index);
-            }
-        }
-        // ========================================
-        // STEP 3: Process each comment range by ID
-        // ========================================
-        for (const [id, startXmlPos] of starts) {
-            const endXmlPos = ends.get(id);
-            // Missing end marker - skip with warning
-            if (endXmlPos === undefined) {
-                console.warn(`Comment ${id}: missing end marker`);
-                continue;
-            }
-            // Calculate text position
-            const docPosition = xmlPosToTextPos(startXmlPos);
-            // Handle empty or inverted ranges
-            if (endXmlPos <= startXmlPos) {
-                anchors.set(id, {
-                    anchor: '',
-                    before: getContextBefore(docPosition),
-                    after: getContextAfter(docPosition),
-                    docPosition,
-                    docLength: fullDocText.length,
-                    isEmpty: true
-                });
-                continue;
-            }
-            // Extract XML segment between markers
-            const segment = docXml.slice(startXmlPos, endXmlPos);
-            // Extract text from w:t (regular) AND w:delText (deleted text in track changes)
-            const textInRangePattern = /<w:t[^>]*>([^<]*)<\/w:t>|<w:delText[^>]*>([^<]*)<\/w:delText>/g;
-            let anchorText = '';
-            let tm;
-            while ((tm = textInRangePattern.exec(segment)) !== null) {
-                anchorText += tm[1] || tm[2] || '';
-            }
-            anchorText = decodeXmlEntities(anchorText);
-            // Get context
-            const anchorLength = anchorText.length;
-            const before = getContextBefore(docPosition);
-            const after = getContextAfter(docPosition + anchorLength);
-            // ALWAYS add entry (even if anchor is empty)
-            anchors.set(id, {
-                anchor: anchorText.trim(),
-                before,
-                after,
-                docPosition,
-                docLength: fullDocText.length,
-                isEmpty: !anchorText.trim()
-            });
-        }
-    }
-    catch (err) {
-        console.error('Error extracting comment anchors:', err.message);
+    const zip = openDocx(docxPath);
+    const { fullDocText, comments } = buildCommentAnchorModel(zip);
+    if (!fullDocText && comments.length === 0) {
         return { anchors, fullDocText: '' };
     }
+    // Context surrounding the anchor, taken from the same plain-text coordinate
+    // system as docPosition so the placement engine can compare like with like.
+    function getContextBefore(position, maxLength = 150) {
+        const beforeText = fullDocText.slice(Math.max(0, position - maxLength), position);
+        const sentenceStart = beforeText.search(/[.!?]\s+[A-Z][^.!?]*$/);
+        return sentenceStart >= 0
+            ? beforeText.slice(sentenceStart + 2).trim()
+            : beforeText.slice(-80).trim();
+    }
+    function getContextAfter(position, maxLength = 150) {
+        const afterText = fullDocText.slice(position, position + maxLength);
+        const sentenceEnd = afterText.search(/[.!?]\s/);
+        return sentenceEnd >= 0
+            ? afterText.slice(0, sentenceEnd + 1).trim()
+            : afterText.slice(0, 80).trim();
+    }
+    for (const range of comments) {
+        anchors.set(range.id, {
+            anchor: range.anchor,
+            before: getContextBefore(range.start),
+            after: getContextAfter(range.end),
+            docPosition: range.start,
+            docLength: fullDocText.length,
+            isEmpty: range.isEmpty,
+        });
+    }
     return { anchors, fullDocText };
 }
 /**
@@ -287,71 +80,19 @@ export async function extractCommentAnchors(docxPath) {
  * concatenated.
  */
 export async function extractHeadings(docxPath) {
-    const AdmZip = (await import('adm-zip')).default;
     if (!fs.existsSync(docxPath)) {
         throw new Error(`File not found: ${docxPath}`);
     }
-    const zip = new AdmZip(docxPath);
-    const docEntry = zip.getEntry('word/document.xml');
-    if (!docEntry)
+    const zip = openDocx(docxPath);
+    const docXml = readPartText(zip, 'word/document.xml');
+    if (docXml === null)
         return [];
-    const xml = docEntry.getData().toString('utf8');
-    // Build the same xml-pos → text-pos mapping that extractCommentAnchors does
-    const textNodePattern = /<w:t[^>]*>([^<]*)<\/w:t>/g;
-    const nodes = [];
-    let textPos = 0;
-    let m;
-    while ((m = textNodePattern.exec(xml)) !== null) {
-        const decoded = decodeXmlEntities(m[1] ?? '');
-        nodes.push({
-            xmlStart: m.index,
-            xmlEnd: m.index + m[0].length,
-            textStart: textPos,
-            textEnd: textPos + decoded.length,
-        });
-        textPos += decoded.length;
-    }
-    function xmlToTextPos(xmlPos) {
-        for (const n of nodes) {
-            if (xmlPos >= n.xmlStart && xmlPos < n.xmlEnd)
-                return n.textStart;
-            if (xmlPos < n.xmlStart)
-                return n.textStart;
-        }
-        return nodes.length ? nodes[nodes.length - 1].textEnd : 0;
-    }
-    const headings = [];
-    const paraPattern = /<w:p\b[^>]*>([\s\S]*?)<\/w:p>/g;
-    let pm;
-    while ((pm = paraPattern.exec(xml)) !== null) {
-        const inner = pm[1];
-        const styleMatch = inner.match(/<w:pStyle[^>]*w:val="([^"]+)"/);
-        if (!styleMatch)
-            continue;
-        const style = styleMatch[1];
-        if (!/heading/i.test(style))
-            continue;
-        // Concatenate text runs; include w:delText so a heading inside a tracked
-        // deletion is still surfaced (verifying anchors against an original draft)
-        const textInRange = /<w:t[^>]*>([^<]*)<\/w:t>|<w:delText[^>]*>([^<]*)<\/w:delText>/g;
-        let txt = '';
-        let tm;
-        while ((tm = textInRange.exec(inner)) !== null) {
-            txt += decodeXmlEntities(tm[1] || tm[2] || '');
-        }
-        const trimmed = txt.trim();
-        if (!trimmed)
-            continue;
-        const levelMatch = style.match(/(\d+)/);
-        const level = levelMatch ? parseInt(levelMatch[1], 10) : 0;
-        headings.push({
-            style,
-            level,
-            text: trimmed,
-            docPosition: xmlToTextPos(pm.index),
-        });
-    }
-    return headings;
+    return buildDocTextModel(docXml).headings.map((h) => ({
+        style: h.style,
+        level: h.level,
+        text: h.text,
+        docPosition: h.position,
+    }));
 }
 /**
  * Decode XML entities in text