@wanshi-kg/wanshi 0.1.0

package/dist/core/processor/readers/TranscriptReader.js

@@ -0,0 +1,234 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.TranscriptReader = void 0;
+const fs = __importStar(require("fs"));
+const FileReader_1 = require("./FileReader");
+const turnPacking_1 = require("./transcript/turnPacking");
+/** Speaker-labeled plain-text transcripts (recua `.parakeet.txt`, etc.). */
+const TEXT_SUFFIXES = [
+    ".parakeet.txt",
+    ".whisper.txt",
+    ".corrected.txt",
+    ".transcript.txt",
+];
+/**
+ * Reads conversational transcripts into **size-packed** chunks (capped at
+ * `maxChunkSize`, tied to the global `chunkSize`) so a long dialogue becomes a
+ * handful of chunks instead of one-per-turn. Each turn is rendered inline as
+ * `speaker: text` so attribution stays visible to the model, and chunk
+ * provenance carries the speaker whenever a chunk happens to be single-speaker.
+ *
+ * Handles three real shapes:
+ *  - recua speaker-labeled text  (`SPEAKER_XX: …` blocks)
+ *  - recua turns JSON            (`[{ start, end, speaker, <backend>: text }]`)
+ *  - Claude/ChatGPT chat export  (`[{ chat_messages: [{ sender, created_at, … }] }]`)
+ *
+ * Registered before JsonFileReader/TextReader; `canRead` claims only files that
+ * sniff as transcripts, deferring everything else.
+ */
+class TranscriptReader extends FileReader_1.FileReader {
+    constructor(chunker, logger, maxChunkSize = 4000) {
+        super([], chunker, logger); // extension list unused; canRead is overridden
+        this.maxChunkSize = maxChunkSize;
+    }
+    getName() {
+        return "TranscriptReader";
+    }
+    adapterId() {
+        return "transcript";
+    }
+    canRead(filePath) {
+        const lower = filePath.toLowerCase();
+        if (TEXT_SUFFIXES.some((s) => lower.endsWith(s)))
+            return true;
+        if (lower.endsWith(".json"))
+            return this.sniffJsonTranscript(filePath);
+        return false;
+    }
+    /** Cheap content sniff (first 8 KB) to claim only transcript-shaped JSON. */
+    sniffJsonTranscript(filePath) {
+        try {
+            const fd = fs.openSync(filePath, "r");
+            const buf = Buffer.alloc(8192);
+            const n = fs.readSync(fd, buf, 0, 8192, 0);
+            fs.closeSync(fd);
+            const head = buf.toString("utf8", 0, n);
+            // Claude/ChatGPT export
+            if (head.includes('"chat_messages"') && head.includes('"sender"'))
+                return true;
+            // recua turns array
+            if (/"speaker"\s*:/.test(head) &&
+                /"start"\s*:/.test(head) &&
+                /"end"\s*:/.test(head))
+                return true;
+            return false;
+        }
+        catch (_a) {
+            return false;
+        }
+    }
+    read(filePath) {
+        return __awaiter(this, void 0, void 0, function* () {
+            const raw = yield fs.promises.readFile(filePath, "utf-8");
+            let turns;
+            try {
+                turns = this.parse(filePath, raw);
+            }
+            catch (e) {
+                this.logger.warn(`TranscriptReader could not parse ${filePath}; falling back to plain chunking: ${e}`);
+                return this.plainFallback(raw);
+            }
+            if (turns.length === 0)
+                return this.plainFallback(raw);
+            const chunks = yield (0, turnPacking_1.packTurns)(turns, filePath, this.maxChunkSize, this.chunker);
+            return {
+                chunks,
+                metadata: { type: "transcript", source: filePath, turns: turns.length },
+            };
+        });
+    }
+    parse(filePath, raw) {
+        var _a, _b;
+        if (filePath.toLowerCase().endsWith(".json")) {
+            const data = JSON.parse(raw);
+            if (Array.isArray(data) && ((_a = data[0]) === null || _a === void 0 ? void 0 : _a.chat_messages) !== undefined) {
+                return this.parseChatExport(data);
+            }
+            if (Array.isArray(data) && ((_b = data[0]) === null || _b === void 0 ? void 0 : _b.speaker) !== undefined) {
+                return this.parseRecuaTurns(data);
+            }
+            throw new Error("unrecognized transcript JSON shape");
+        }
+        return this.parseSpeakerText(raw);
+    }
+    /** "SPEAKER_XX: text" blocks separated by blank lines. */
+    parseSpeakerText(raw) {
+        const labelRe = /^([A-Za-z0-9_][\w .\-]{0,40}?):\s+/;
+        const blocks = raw
+            .split(/\n\s*\n/)
+            .map((b) => b.trim())
+            .filter(Boolean);
+        const turns = [];
+        for (const block of blocks) {
+            const m = block.match(labelRe);
+            if (m) {
+                turns.push({ speaker: m[1].trim(), text: block.slice(m[0].length).trim() });
+            }
+            else if (turns.length > 0) {
+                turns[turns.length - 1].text += " " + block; // continuation
+            }
+            else {
+                turns.push({ speaker: "UNKNOWN", text: block });
+            }
+        }
+        return turns;
+    }
+    parseRecuaTurns(data) {
+        return data
+            .map((t) => {
+            var _a;
+            return ({
+                speaker: String((_a = t.speaker) !== null && _a !== void 0 ? _a : "UNKNOWN"),
+                text: this.pickRecuaText(t),
+            });
+        })
+            .filter((t) => t.text);
+    }
+    pickRecuaText(t) {
+        for (const k of ["corrected", "parakeet", "whisper"]) {
+            if (typeof t[k] === "string" && t[k].trim())
+                return t[k].trim();
+        }
+        for (const [k, v] of Object.entries(t)) {
+            if (k === "start" || k === "end" || k === "speaker")
+                continue;
+            if (typeof v === "string" && v.trim())
+                return v.trim();
+        }
+        return "";
+    }
+    parseChatExport(convs) {
+        const turns = [];
+        convs.forEach((conv, convIndex) => {
+            var _a, _b;
+            for (const msg of (_a = conv.chat_messages) !== null && _a !== void 0 ? _a : []) {
+                const text = this.chatMessageText(msg);
+                if (!text)
+                    continue;
+                turns.push({
+                    speaker: String((_b = msg.sender) !== null && _b !== void 0 ? _b : "unknown"),
+                    text,
+                    occurredAt: typeof msg.created_at === "string" ? msg.created_at : undefined,
+                    // Tag each turn with its conversation so chunkTurns never packs two
+                    // conversations together (cross-conversation fact bleed, KG-10).
+                    conversation: convIndex,
+                });
+            }
+        });
+        return turns;
+    }
+    chatMessageText(msg) {
+        if (typeof msg.text === "string" && msg.text.trim())
+            return msg.text.trim();
+        if (Array.isArray(msg.content)) {
+            return msg.content
+                .map((c) => (typeof (c === null || c === void 0 ? void 0 : c.text) === "string" ? c.text : ""))
+                .join(" ")
+                .trim();
+        }
+        return "";
+    }
+    plainFallback(raw) {
+        return __awaiter(this, void 0, void 0, function* () {
+            const parts = yield this.chunker.chunk(raw);
+            return {
+                chunks: parts.map((p) => (Object.assign({}, p))),
+                metadata: { type: "transcript-fallback" },
+            };
+        });
+    }
+}
+exports.TranscriptReader = TranscriptReader;
+//# sourceMappingURL=TranscriptReader.js.map

package/dist/core/processor/readers/TranscriptReader.js.map

@@ -0,0 +1 @@
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package/dist/core/processor/readers/image/imageMetadata.js

@@ -0,0 +1,155 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.readExif = readExif;
+exports.readC2pa = readC2pa;
+const child_process_1 = require("child_process");
+/**
+ * Read EXIF metadata from an image via `exifr` (pure-JS). Returns `undefined`
+ * when the image has no usable EXIF (e.g. a PNG screenshot) or on any parse
+ * error — extraction is an enhancement, never a failure mode. Lazy-imports
+ * `exifr` so a run that never touches an image pays nothing.
+ */
+function readExif(filePath, logger) {
+    return __awaiter(this, void 0, void 0, function* () {
+        var _a, _b, _c, _d;
+        try {
+            const exifr = yield Promise.resolve().then(() => __importStar(require("exifr")));
+            const parse = (_a = exifr.parse) !== null && _a !== void 0 ? _a : (_b = exifr.default) === null || _b === void 0 ? void 0 : _b.parse;
+            // Block selectors: tiff (IFD0: Make/Model/Artist/Software) + exif (DateTimeOriginal)
+            // + gps (so exifr computes decimal latitude/longitude).
+            const o = yield parse(filePath, { tiff: true, exif: true, gps: true });
+            if (!o)
+                return undefined;
+            const meta = {};
+            if (typeof o.latitude === "number" && typeof o.longitude === "number") {
+                meta.gps = { lat: o.latitude, lng: o.longitude };
+            }
+            const dt = (_d = (_c = o.DateTimeOriginal) !== null && _c !== void 0 ? _c : o.CreateDate) !== null && _d !== void 0 ? _d : o.ModifyDate;
+            if (dt)
+                meta.dateTaken = dt instanceof Date ? dt.toISOString() : String(dt);
+            const make = typeof o.Make === "string" ? o.Make.trim() : undefined;
+            const model = typeof o.Model === "string" ? o.Model.trim() : undefined;
+            if (make || model)
+                meta.camera = Object.assign(Object.assign({}, (make ? { make } : {})), (model ? { model } : {}));
+            if (typeof o.Artist === "string" && o.Artist.trim())
+                meta.author = o.Artist.trim();
+            if (typeof o.Software === "string" && o.Software.trim())
+                meta.software = o.Software.trim();
+            return Object.keys(meta).length ? meta : undefined;
+        }
+        catch (e) {
+            logger === null || logger === void 0 ? void 0 : logger.debug(`EXIF read failed for ${filePath}: ${e}`);
+            return undefined;
+        }
+    });
+}
+/**
+ * Read C2PA Content Credentials by shelling the official Adobe/CAI `c2patool`
+ * (reference-grade cryptographic validation; degrade-if-absent like marker). Never
+ * throws — a missing binary / parse error yields `{present:false, unavailable:true}`.
+ */
+function readC2pa(filePath_1) {
+    return __awaiter(this, arguments, void 0, function* (filePath, command = "c2patool", logger) {
+        try {
+            const { code, stdout, stderr } = yield runCommand(command, [filePath], 30000);
+            if (code !== 0) {
+                // c2patool exits non-zero with "No claim found" when the asset has no
+                // credential — a real fact (absent), distinct from the tool being missing.
+                if (/no (claim|manifest|provenance|c2pa)/i.test(`${stderr}\n${stdout}`))
+                    return { present: false };
+                logger === null || logger === void 0 ? void 0 : logger.debug(`c2patool exited ${code} for ${filePath}: ${stderr.trim().slice(-200)}`);
+                return { present: false, unavailable: true };
+            }
+            return parseC2pa(JSON.parse(stdout));
+        }
+        catch (e) {
+            // ENOENT (binary not installed), timeout, or unparseable output → we could not
+            // read provenance. Distinct from "no credential present".
+            logger === null || logger === void 0 ? void 0 : logger.debug(`C2PA read unavailable for ${filePath}: ${e}`);
+            return { present: false, unavailable: true };
+        }
+    });
+}
+/** Map a c2patool manifest-store JSON report to the trust facts we record. */
+function parseC2pa(json) {
+    var _a, _b;
+    const manifests = (_a = json === null || json === void 0 ? void 0 : json.manifests) !== null && _a !== void 0 ? _a : {};
+    const active = json === null || json === void 0 ? void 0 : json.active_manifest;
+    const present = !!active || Object.keys(manifests).length > 0;
+    if (!present)
+        return { present: false };
+    const m = (active && manifests[active]) || Object.values(manifests)[0] || {};
+    const sigInfo = (_b = m === null || m === void 0 ? void 0 : m.signature_info) !== null && _b !== void 0 ? _b : {};
+    const signer = typeof sigInfo.issuer === "string" ? sigInfo.issuer : typeof sigInfo.common_name === "string" ? sigInfo.common_name : undefined;
+    const vstatus = Array.isArray(json === null || json === void 0 ? void 0 : json.validation_status) ? json.validation_status : [];
+    const valid = vstatus.every((v) => { var _a; return !/error|invalid|fail/i.test(String((_a = v === null || v === void 0 ? void 0 : v.code) !== null && _a !== void 0 ? _a : "")); });
+    // C2PA's AI-generation indicator (digitalSourceType …trainedAlgorithmicMedia).
+    const aiGenerated = /trainedAlgorithmicMedia/i.test(JSON.stringify(json));
+    return { present: true, valid, signer, aiGenerated };
+}
+/** Spawn a CLI with captured output + timeout; rejects on launch error (ENOENT). */
+function runCommand(command, args, timeoutMs) {
+    return new Promise((resolve, reject) => {
+        var _a, _b;
+        const child = (0, child_process_1.spawn)(command, args, { stdio: ["ignore", "pipe", "pipe"] });
+        let stdout = "";
+        let stderr = "";
+        (_a = child.stdout) === null || _a === void 0 ? void 0 : _a.on("data", (d) => (stdout += d.toString()));
+        (_b = child.stderr) === null || _b === void 0 ? void 0 : _b.on("data", (d) => (stderr += d.toString()));
+        const timer = setTimeout(() => {
+            child.kill("SIGTERM");
+            reject(new Error(`${command} timed out after ${timeoutMs}ms`));
+        }, timeoutMs);
+        child.on("error", (e) => {
+            clearTimeout(timer);
+            reject(e);
+        });
+        child.on("close", (code) => {
+            clearTimeout(timer);
+            resolve({ code: code !== null && code !== void 0 ? code : 0, stdout, stderr });
+        });
+    });
+}
+//# sourceMappingURL=imageMetadata.js.map

package/dist/core/processor/readers/image/imageMetadata.js.map

@@ -0,0 +1 @@
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package/dist/core/processor/readers/index.js

@@ -0,0 +1,41 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+__exportStar(require("./AudioReader"), exports);
+__exportStar(require("./BinaryReader"), exports);
+__exportStar(require("./ChandraPdfReader"), exports);
+__exportStar(require("./ChatExportReader"), exports);
+__exportStar(require("./DoclingReader"), exports);
+__exportStar(require("./EmailReader"), exports);
+__exportStar(require("./EpubReader"), exports);
+__exportStar(require("./FileReader"), exports);
+__exportStar(require("./FileReaderFactory"), exports);
+__exportStar(require("./HtmlReader"), exports);
+__exportStar(require("./ImageReader"), exports);
+__exportStar(require("./JsonFileReader"), exports);
+__exportStar(require("./JupyterReader"), exports);
+__exportStar(require("./LatexReader"), exports);
+__exportStar(require("./MarkdownReader"), exports);
+__exportStar(require("./MarkerPdfReader"), exports);
+__exportStar(require("./MistralOcrReader"), exports);
+__exportStar(require("./OfficeReader"), exports);
+__exportStar(require("./PdfReader"), exports);
+__exportStar(require("./RtfReader"), exports);
+__exportStar(require("./SubtitleReader"), exports);
+__exportStar(require("./TesseractPdfReader"), exports);
+__exportStar(require("./TextReader"), exports);
+__exportStar(require("./TranscriptReader"), exports);
+//# sourceMappingURL=index.js.map

package/dist/core/processor/readers/index.js.map

@@ -0,0 +1 @@
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package/dist/core/processor/readers/referenceExtraction.js

@@ -0,0 +1,198 @@
+"use strict";
+/**
+ * Reader-side raw reference extraction (Phase 0, network-free).
+ *
+ * Pure functions that pull the *references a document already contains* out of
+ * its source text — internal links (markdown `[t](u)`, `[[wikilinks]]`, HTML
+ * `href`) and citations (a trailing bibliography block + inline arXiv/DOI/PMID).
+ * Nothing here resolves or fetches: readers stash the raw result on
+ * `metadata.references` and the corpus-level `ReferenceResolver` turns it into
+ * `links_to` / `cites` edges once the full file set is known.
+ *
+ * Citation parsing is hybrid: Citation.js handles structured BibTeX/`.bib`
+ * blocks; a regex fallback handles prose bibliographies (the common case) and
+ * inline ids. Citation.js throwing on prose is expected and caught.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.isExternalTarget = isExternalTarget;
+exports.extractMarkdownLinks = extractMarkdownLinks;
+exports.extractHtmlLinks = extractHtmlLinks;
+exports.extractBareUrls = extractBareUrls;
+exports.extractCitations = extractCitations;
+let citeCtor;
+function loadCite() {
+    if (citeCtor !== undefined)
+        return citeCtor;
+    try {
+        const core = require("@citation-js/core");
+        require("@citation-js/plugin-bibtex"); // side-effect: registers the @biblatex input
+        citeCtor = core.Cite;
+    }
+    catch (_a) {
+        citeCtor = null;
+    }
+    return citeCtor;
+}
+// --- ID patterns (global; reused for block + inline scans) --------------------
+const ARXIV_RE = /arxiv:\s*(\d{4}\.\d{4,5}(?:v\d+)?)/gi;
+const DOI_RE = /\b10\.\d{4,9}\/[-._;()/:a-z0-9]+/gi;
+const PMID_RE = /\bpmid:\s*(\d{1,9})\b/gi;
+const REF_HEADING_RE = /^(?:#{1,6}\s*)?(?:[\divxlc]+\.?\s+)?(references|bibliography|works cited)\s*:?\s*$/i;
+/** Strip trailing punctuation a DOI/URL regex commonly over-captures. */
+function trimTrailingPunct(s) {
+    return s.replace(/[.,;:)\]]+$/, "");
+}
+/** http(s)/protocol-relative/mailto/tel/data targets — external, not a corpus file. */
+function isExternalTarget(target) {
+    return /^(?:[a-z][a-z0-9+.-]*:|\/\/)/i.test(target);
+}
+// --- Internal links -----------------------------------------------------------
+/** Markdown inline links `[text](target)` (excluding `![images]`) + `[[wikilinks]]`. */
+function extractMarkdownLinks(text) {
+    var _a;
+    const links = [];
+    // `[text](target ...)` but not image `![text](...)`; ignore pure `#fragment`.
+    const inline = /(?<!!)\[([^\]]*)\]\(\s*([^)\s]+)[^)]*\)/g;
+    for (const m of text.matchAll(inline)) {
+        const target = m[2].trim();
+        if (!target || target.startsWith("#"))
+            continue;
+        links.push({ target, text: m[1].trim() || undefined, kind: "markdown" });
+    }
+    // `[[target]]` or `[[target|alias]]`.
+    const wiki = /\[\[([^\]|]+?)(?:\|([^\]]+))?\]\]/g;
+    for (const m of text.matchAll(wiki)) {
+        const target = m[1].trim();
+        if (!target)
+            continue;
+        links.push({ target, text: ((_a = m[2]) === null || _a === void 0 ? void 0 : _a.trim()) || undefined, kind: "wikilink" });
+    }
+    return links;
+}
+/** Anchor `href`s from raw HTML; ignores pure `#fragment` links. */
+function extractHtmlLinks(html) {
+    const links = [];
+    const anchor = /<a\b[^>]*\bhref\s*=\s*["']([^"']+)["'][^>]*>([\s\S]*?)<\/a>/gi;
+    for (const m of html.matchAll(anchor)) {
+        const target = m[1].trim();
+        if (!target || target.startsWith("#"))
+            continue;
+        const text = m[2].replace(/<[^>]+>/g, "").trim();
+        links.push({ target, text: text || undefined, kind: "html" });
+    }
+    return links;
+}
+/**
+ * Bare absolute URLs anywhere in the text — `> source: https://…` web-clip
+ * frontmatter, `Source: …` lines, and inline bare links the markdown-link regex
+ * misses (web clips often flatten `[t](u)` to plain text + a source header).
+ * These are external by construction; the Phase-1 fetcher consumes them (gated
+ * by the allowlist), the Phase-0 resolver ignores them.
+ */
+function extractBareUrls(text) {
+    const seen = new Set();
+    const out = [];
+    for (const m of text.matchAll(/\bhttps?:\/\/[^\s)<>"'\]}|]+/gi)) {
+        const target = m[0].replace(/[.,;:]+$/, "");
+        if (seen.has(target))
+            continue;
+        seen.add(target);
+        out.push({ target, kind: "url" });
+    }
+    return out;
+}
+// --- Citations ----------------------------------------------------------------
+function citationKey(c) {
+    var _a, _b, _c, _d, _e, _f, _g;
+    return ((_g = (_e = (_d = (_b = (_a = c.arxivId) === null || _a === void 0 ? void 0 : _a.toLowerCase()) !== null && _b !== void 0 ? _b : (_c = c.doi) === null || _c === void 0 ? void 0 : _c.toLowerCase()) !== null && _d !== void 0 ? _d : (c.pmid ? `pmid:${c.pmid}` : undefined)) !== null && _e !== void 0 ? _e : (_f = c.title) === null || _f === void 0 ? void 0 : _f.toLowerCase()) !== null && _g !== void 0 ? _g : c.raw.toLowerCase());
+}
+/** Pull arXiv-id / DOI / PMID out of a single reference string. */
+function extractIds(s) {
+    const arxiv = new RegExp(ARXIV_RE.source, "i").exec(s);
+    const doi = new RegExp(DOI_RE.source, "i").exec(s);
+    const pmid = new RegExp(PMID_RE.source, "i").exec(s);
+    return Object.assign(Object.assign(Object.assign({}, (arxiv ? { arxivId: arxiv[1] } : {})), (doi ? { doi: trimTrailingPunct(doi[0]) } : {})), (pmid ? { pmid: pmid[1] } : {}));
+}
+/** Structured parse via Citation.js; returns [] (not throw) on non-BibTeX input. */
+function parseStructured(block) {
+    var _a;
+    if (!/@\w+\s*\{/.test(block))
+        return []; // cheap guard: looks like BibTeX?
+    const Cite = loadCite();
+    if (!Cite)
+        return [];
+    try {
+        const entries = (_a = new Cite(block).data) !== null && _a !== void 0 ? _a : [];
+        return entries
+            .map((e) => {
+            var _a;
+            const raw = ((_a = e.title) !== null && _a !== void 0 ? _a : "").toString().trim();
+            return Object.assign(Object.assign({ raw: raw || JSON.stringify(e).slice(0, 200) }, (e.title ? { title: String(e.title) } : {})), (e.DOI ? { doi: String(e.DOI) } : {}));
+        })
+            .filter((c) => c.raw.length > 0);
+    }
+    catch (_b) {
+        return [];
+    }
+}
+/** Split a prose bibliography block into entries, marker-aware with line fallback. */
+function splitProseEntries(block) {
+    const lines = block
+        .split("\n")
+        .filter((l, i) => !(i === 0 && REF_HEADING_RE.test(l.trim()))) // drop a leading heading
+        .map((l) => l.trim());
+    const marker = /^\s*(?:\[\d+\]|\(\d+\)|\d+[.)])\s+/;
+    const hasMarkers = lines.some((l) => marker.test(l));
+    if (hasMarkers) {
+        const entries = [];
+        for (const line of lines) {
+            if (!line)
+                continue;
+            if (marker.test(line))
+                entries.push(line.replace(marker, ""));
+            else if (entries.length)
+                entries[entries.length - 1] += ` ${line}`;
+            else
+                entries.push(line);
+        }
+        return entries;
+    }
+    // No numbering: one entry per non-empty line.
+    return lines.filter(Boolean);
+}
+/**
+ * Extract citations from a (possibly undefined) trailing references block plus
+ * inline arXiv/DOI ids found anywhere in the body. Deduped by id/title.
+ */
+function extractCitations(referencesBlock, bodyText) {
+    const out = new Map();
+    const add = (c) => {
+        const key = citationKey(c);
+        if (key && !out.has(key))
+            out.set(key, c);
+    };
+    if (referencesBlock && referencesBlock.trim()) {
+        const structured = parseStructured(referencesBlock);
+        if (structured.length) {
+            structured.forEach((c) => { var _a; return add(Object.assign(Object.assign({}, c), extractIds(c.raw + " " + ((_a = c.doi) !== null && _a !== void 0 ? _a : "")))); });
+        }
+        else {
+            for (const entry of splitProseEntries(referencesBlock)) {
+                const ids = extractIds(entry);
+                add(Object.assign({ raw: entry.slice(0, 300) }, ids));
+            }
+        }
+    }
+    // Inline ids in the body (e.g. "see arXiv:2001.12345") that aren't in the list.
+    for (const m of bodyText.matchAll(new RegExp(ARXIV_RE.source, "gi"))) {
+        add({ raw: m[0], arxivId: m[1] });
+    }
+    for (const m of bodyText.matchAll(new RegExp(DOI_RE.source, "gi"))) {
+        add({ raw: m[0], doi: trimTrailingPunct(m[0]) });
+    }
+    for (const m of bodyText.matchAll(new RegExp(PMID_RE.source, "gi"))) {
+        add({ raw: m[0], pmid: m[1] });
+    }
+    return Array.from(out.values());
+}
+//# sourceMappingURL=referenceExtraction.js.map