docrev 0.10.2 → 0.11.0

package/dist/lib/rate-limiter.d.ts

@@ -6,12 +6,20 @@ export interface RateLimiterOptions {
     maxDelay?: number;
     maxRetries?: number;
     backoffFactor?: number;
+    /** Per-request timeout in ms; a stalled connection aborts instead of hanging. */
+    requestTimeout?: number;
 }
+/**
+ * Parse an HTTP `Retry-After` header, which may be a delay in seconds or an
+ * HTTP-date. Returns the delay in milliseconds, or null when unparseable.
+ */
+export declare function parseRetryAfter(value: string | null, now?: number): number | null;
 export declare class RateLimiter {
     private minDelay;
     private maxDelay;
     private maxRetries;
     private backoffFactor;
+    private requestTimeout;
     private lastRequestTime;
     private currentDelay;
     private consecutiveErrors;

package/dist/lib/rate-limiter.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"rate-limiter.d.ts","sourceRoot":"","sources":["../../lib/rate-limiter.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,MAAM,WAAW,kBAAkB;IACjC,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,iFAAiF;IACjF,cAAc,CAAC,EAAE,MAAM,CAAC;CACzB;AAED;;;GAGG;AACH,wBAAgB,eAAe,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,EAAE,GAAG,GAAE,MAAmB,GAAG,MAAM,GAAG,IAAI,CAO7F;AAED,qBAAa,WAAW;IACtB,OAAO,CAAC,QAAQ,CAAS;IACzB,OAAO,CAAC,QAAQ,CAAS;IACzB,OAAO,CAAC,UAAU,CAAS;IAC3B,OAAO,CAAC,aAAa,CAAS;IAC9B,OAAO,CAAC,cAAc,CAAS;IAC/B,OAAO,CAAC,eAAe,CAAS;IAChC,OAAO,CAAC,YAAY,CAAS;IAC7B,OAAO,CAAC,iBAAiB,CAAS;gBAEtB,OAAO,GAAE,kBAAuB;IAWtC,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC;IAS3B,SAAS,IAAI,IAAI;IAMjB,OAAO,CAAC,UAAU,EAAE,MAAM,GAAG,OAAO;IAS9B,cAAc,CAAC,GAAG,EAAE,MAAM,EAAE,OAAO,GAAE,WAAgB,GAAG,OAAO,CAAC,QAAQ,CAAC;CAkDhF;AAGD,eAAO,MAAM,eAAe,aAAsD,CAAC;AACnF,eAAO,MAAM,eAAe,aAAsD,CAAC;AACnF,eAAO,MAAM,aAAa,aAAsD,CAAC"}

package/dist/lib/rate-limiter.js

@@ -1,11 +1,27 @@
 /**
  * Rate Limiter - Prevents API abuse with exponential backoff
  */
+/**
+ * Parse an HTTP `Retry-After` header, which may be a delay in seconds or an
+ * HTTP-date. Returns the delay in milliseconds, or null when unparseable.
+ */
+export function parseRetryAfter(value, now = Date.now()) {
+    if (!value)
+        return null;
+    const seconds = Number(value);
+    if (Number.isFinite(seconds))
+        return Math.max(0, seconds * 1000);
+    const date = Date.parse(value);
+    if (!Number.isNaN(date))
+        return Math.max(0, date - now);
+    return null;
+}
 export class RateLimiter {
     minDelay;
     maxDelay;
     maxRetries;
     backoffFactor;
+    requestTimeout;
     lastRequestTime;
     currentDelay;
     consecutiveErrors;
@@ -14,6 +30,7 @@ export class RateLimiter {
         this.maxDelay = options.maxDelay || 30000; // Max delay after backoff (ms)
         this.maxRetries = options.maxRetries || 3; // Max retry attempts
         this.backoffFactor = options.backoffFactor || 2;
+        this.requestTimeout = options.requestTimeout || 15000; // Abort a stalled request
         this.lastRequestTime = 0;
         this.currentDelay = this.minDelay;
         this.consecutiveErrors = 0;
@@ -41,14 +58,25 @@ export class RateLimiter {
     }
     async fetchWithRetry(url, options = {}) {
         let lastError;
+        const callerSignal = options.signal ?? undefined;
         for (let attempt = 0; attempt <= this.maxRetries; attempt++) {
             await this.wait();
+            // Bound each attempt so a half-open connection cannot hang the run
+            // forever; merge the caller's signal so an external cancel still works.
+            const controller = new AbortController();
+            const timer = setTimeout(() => controller.abort(new Error('Request timed out')), this.requestTimeout);
+            const onCallerAbort = () => controller.abort(callerSignal.reason);
+            if (callerSignal) {
+                if (callerSignal.aborted)
+                    controller.abort(callerSignal.reason);
+                else
+                    callerSignal.addEventListener('abort', onCallerAbort, { once: true });
+            }
             try {
-                const response = await fetch(url, options);
+                const response = await fetch(url, { ...options, signal: controller.signal });
                 if (response.status === 429) {
-                    // Rate limited - back off
-                    const retryAfter = response.headers.get('Retry-After');
-                    const delay = retryAfter ? parseInt(retryAfter, 10) * 1000 : this.currentDelay * 2;
+                    // Rate limited - back off. Retry-After may be seconds or an HTTP-date.
+                    const delay = parseRetryAfter(response.headers.get('Retry-After')) ?? this.currentDelay * 2;
                     this.currentDelay = Math.min(this.maxDelay, delay);
                     if (!this.onError(429))
                         break;
@@ -64,10 +92,19 @@ export class RateLimiter {
                 return response;
             }
             catch (err) {
+                // A caller-initiated abort is intentional cancellation, not a failure
+                // to retry around.
+                if (callerSignal?.aborted)
+                    throw err;
                 lastError = err;
                 if (!this.onError(0))
                     break;
             }
+            finally {
+                clearTimeout(timer);
+                if (callerSignal)
+                    callerSignal.removeEventListener('abort', onCallerAbort);
+            }
         }
         throw lastError || new Error('Max retries exceeded');
     }

package/dist/lib/rate-limiter.js.map

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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

@@ -1 +1 @@
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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