paper-manager 0.1.0

package/LICENSE

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+MIT License
+
+Copyright (c) 2026 Phantom
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

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+# my-ts-starter
+
+A minimal TypeScript project template with modern tooling powered by the [oxc](https://oxc.rs/) ecosystem.
+
+## Features
+
+- **TypeScript** — Type-safe development with `tsc`
+- **oxlint** — Fast linter with type-aware rules (via `oxlint-tsgolint`)
+- **oxfmt** — Fast formatter
+
+## Getting Started
+
+```bash
+# Install dependencies
+pnpm install
+
+# Type check
+pnpm typecheck
+
+# Lint
+pnpm lint
+
+# Format
+pnpm fmt
+```
+
+## Available Scripts
+
+| Script           | Description                      |
+| ---------------- | -------------------------------- |
+| `pnpm typecheck` | Run TypeScript type checking     |
+| `pnpm lint`      | Lint with oxlint (type-aware)    |
+| `pnpm lint:fix`  | Lint and auto-fix                |
+| `pnpm fmt`       | Format with oxfmt                |
+| `pnpm fmt:check` | Check formatting without writing |
+
+## License
+
+[MIT](LICENSE)

package/dist/ai/embed.d.ts

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+import type { EmbeddingModelConfig } from "../types/index.js";
+export declare function embed(config: EmbeddingModelConfig, text: string): Promise<number[]>;
+export declare function embedMany(config: EmbeddingModelConfig, texts: string[]): Promise<number[][]>;

package/dist/ai/embed.js

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+import { embed as aiEmbed, embedMany as aiEmbedMany } from "ai";
+import { createEmbeddingModel } from "./provider.js";
+export async function embed(config, text) {
+    const model = createEmbeddingModel(config);
+    const result = await aiEmbed({ model, value: text });
+    return result.embedding;
+}
+export async function embedMany(config, texts) {
+    const model = createEmbeddingModel(config);
+    const result = await aiEmbedMany({ model, values: texts });
+    return result.embeddings;
+}
+//# sourceMappingURL=embed.js.map

package/dist/ai/embed.js.map

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package/dist/ai/index.d.ts

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+export { embed, embedMany } from "./embed.js";
+export { createEmbeddingModel } from "./provider.js";

package/dist/ai/index.js

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+export { embed, embedMany } from "./embed.js";
+export { createEmbeddingModel } from "./provider.js";
+//# sourceMappingURL=index.js.map

package/dist/ai/index.js.map

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package/dist/ai/provider.d.ts

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+import type { EmbeddingModelV3 } from "@ai-sdk/provider";
+import type { EmbeddingModelConfig } from "../types/index.js";
+export declare function createEmbeddingModel(config: EmbeddingModelConfig): EmbeddingModelV3;

package/dist/ai/provider.js

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+import { createOpenAI } from "@ai-sdk/openai";
+export function createEmbeddingModel(config) {
+    const openai = createOpenAI({
+        apiKey: config.apiKey,
+        baseURL: config.baseUrl,
+    });
+    return openai.embedding(config.model);
+}
+//# sourceMappingURL=provider.js.map

package/dist/ai/provider.js.map

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package/dist/commands/config.d.ts

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+import { Command } from "commander";
+export declare function createConfigCommand(): Command;

package/dist/commands/config.js

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+import { Command } from "commander";
+import { listConfig, loadMergedConfig, removeConfig, setConfig } from "../config/index.js";
+export function createConfigCommand() {
+    const config = new Command("config").description("Manage configuration");
+    config
+        .command("get <key>")
+        .description("Get a config value")
+        .option("--user", "Read from user config")
+        .action((key, options) => {
+        const source = options.user ? listConfig({ user: true }) : loadMergedConfig();
+        const value = source[key];
+        if (value === undefined) {
+            console.log(`Config "${key}" is not set.`);
+        }
+        else {
+            console.log(JSON.stringify(value, null, 2));
+        }
+    });
+    config
+        .command("set <key> <value>")
+        .description("Set a config value")
+        .option("--user", "Write to user config")
+        .action((key, rawValue, options) => {
+        let value;
+        try {
+            value = JSON.parse(rawValue);
+        }
+        catch {
+            value = rawValue;
+        }
+        setConfig(key, value, { user: options.user });
+        console.log(`Config "${key}" has been set.`);
+    });
+    config
+        .command("remove <key>")
+        .description("Remove a config key")
+        .option("--user", "Remove from user config")
+        .action((key, options) => {
+        removeConfig(key, { user: options.user });
+        console.log(`Config "${key}" has been removed.`);
+    });
+    config
+        .command("list")
+        .description("List all config")
+        .option("--user", "List user config only")
+        .action((options) => {
+        const result = options.user ? listConfig({ user: true }) : loadMergedConfig();
+        if (Object.keys(result).length === 0) {
+            console.log("No config set.");
+        }
+        else {
+            console.log(JSON.stringify(result, null, 2));
+        }
+    });
+    return config;
+}
+//# sourceMappingURL=config.js.map

package/dist/commands/config.js.map

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package/dist/commands/knowledge-base.d.ts

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+import { Command } from "commander";
+export declare function createKnowledgeBaseCommand(): Command;

package/dist/commands/knowledge-base.js

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+import * as fs from "node:fs";
+import * as path from "node:path";
+import { Command } from "commander";
+import { getConfig, getModelConfig, getPdfDir, getProjectDataDir, getUserDataDir, getVectorStoreDir, } from "../config/index.js";
+import * as projectKb from "../db/project/knowledge-bases.js";
+import * as projectLit from "../db/project/literatures.js";
+import * as userKb from "../db/user/knowledge-bases.js";
+import * as userLit from "../db/user/literatures.js";
+import { queryVectorStore } from "../vector-store/index.js";
+function resolveKnowledgeBase(id) {
+    const pkb = projectKb.getKnowledgeBase(id);
+    if (pkb)
+        return { kb: pkb, scope: "project" };
+    const ukb = userKb.getKnowledgeBase(id);
+    if (ukb)
+        return { kb: ukb, scope: "user" };
+    return null;
+}
+function getBaseDir(scope) {
+    return scope === "project" ? getProjectDataDir() : getUserDataDir();
+}
+export function createKnowledgeBaseCommand() {
+    const kb = new Command("kb").description("Manage knowledge bases");
+    kb.command("create <name>")
+        .description("Create a knowledge base")
+        .requiredOption("-d, --description <desc>", "Knowledge base description")
+        .option("-e, --embedding-model <id>", "Embedding model config ID")
+        .option("--user", "Create in user scope")
+        .action((name, options) => {
+        let embeddingModelId = options.embeddingModel;
+        if (!embeddingModelId) {
+            const defaultId = getConfig("defaultEmbeddingModelId");
+            if (!defaultId) {
+                console.error("Error: No embedding model specified and no default configured.");
+                process.exit(1);
+            }
+            embeddingModelId = defaultId;
+        }
+        // Validate model config exists
+        const models = getConfig("embeddingModels");
+        if (!models?.[embeddingModelId]) {
+            console.error(`Error: Embedding model "${embeddingModelId}" not found in config.`);
+            process.exit(1);
+        }
+        const create = options.user ? userKb.createKnowledgeBase : projectKb.createKnowledgeBase;
+        const result = create({
+            name,
+            description: options.description,
+            embeddingModelId,
+        });
+        console.log(`Knowledge base created: ${result.id}`);
+        console.log(`  Name: ${result.name}`);
+        console.log(`  Scope: ${options.user ? "user" : "project"}`);
+    });
+    kb.command("list")
+        .description("List knowledge bases")
+        .option("--user", "List user knowledge bases only")
+        .option("--all", "List all knowledge bases (default)")
+        .action((options) => {
+        let results = [];
+        if (options.user) {
+            results = userKb.listKnowledgeBases().map((k) => ({ ...k, scope: "user" }));
+        }
+        else {
+            const projectKbs = projectKb.listKnowledgeBases().map((k) => ({ ...k, scope: "project" }));
+            const userKbs = userKb.listKnowledgeBases().map((k) => ({ ...k, scope: "user" }));
+            results = [...projectKbs, ...userKbs];
+        }
+        if (results.length === 0) {
+            console.log("No knowledge bases found.");
+            return;
+        }
+        for (const kb of results) {
+            console.log(`[${kb.scope}] ${kb.id}`);
+            console.log(`  Name: ${kb.name}`);
+            console.log(`  Description: ${kb.description}`);
+            console.log(`  Model: ${kb.embeddingModelId}`);
+            console.log(`  Created: ${kb.createdAt.toISOString()}`);
+            console.log();
+        }
+    });
+    kb.command("remove <id>")
+        .description("Remove a knowledge base and all its data")
+        .action((id) => {
+        const resolved = resolveKnowledgeBase(id);
+        if (!resolved) {
+            console.error(`Knowledge base not found: ${id}`);
+            process.exit(1);
+        }
+        const { scope } = resolved;
+        const baseDir = getBaseDir(scope);
+        const litOps = scope === "project" ? projectLit : userLit;
+        const kbOps = scope === "project" ? projectKb : userKb;
+        // 1. Get all literatures in this KB
+        const literatures = litOps.getLiteraturesByKnowledgeBaseId(id);
+        // 2. Delete PDF files
+        const pdfDir = getPdfDir(baseDir);
+        for (const lit of literatures) {
+            const pdfPath = path.join(pdfDir, `${lit.id}.pdf`);
+            if (fs.existsSync(pdfPath)) {
+                fs.unlinkSync(pdfPath);
+            }
+        }
+        // 3. Delete literatures from DB
+        litOps.deleteLiteraturesByKnowledgeBaseId(id);
+        // 4. Delete vector store directory
+        const vectorDir = path.join(getVectorStoreDir(baseDir), id);
+        if (fs.existsSync(vectorDir)) {
+            fs.rmSync(vectorDir, { recursive: true });
+        }
+        // 5. Delete knowledge base
+        kbOps.deleteKnowledgeBase(id);
+        console.log(`Knowledge base "${id}" and all associated data removed.`);
+    });
+    kb.command("query <id> <query-text>")
+        .description("Query a knowledge base")
+        .option("-k, --top-k <number>", "Number of results", "5")
+        .action(async (id, queryText, options) => {
+        const resolved = resolveKnowledgeBase(id);
+        if (!resolved) {
+            console.error(`Knowledge base not found: ${id}`);
+            process.exit(1);
+        }
+        const { kb: kbMeta, scope } = resolved;
+        const baseDir = getBaseDir(scope);
+        const vectorDir = path.join(getVectorStoreDir(baseDir), id);
+        if (!fs.existsSync(vectorDir)) {
+            console.error("No vector store found for this knowledge base.");
+            process.exit(1);
+        }
+        const modelConfig = getModelConfig(kbMeta.embeddingModelId);
+        const k = parseInt(options.topK, 10);
+        const results = await queryVectorStore(modelConfig, vectorDir, queryText, k);
+        if (results.length === 0) {
+            console.log("No results found.");
+            return;
+        }
+        for (let i = 0; i < results.length; i++) {
+            const doc = results[i];
+            if (!doc)
+                continue;
+            console.log(`--- Result ${String(i + 1)} ---`);
+            console.log(doc.pageContent);
+            if (doc.metadata && Object.keys(doc.metadata).length > 0) {
+                console.log(`  Metadata: ${JSON.stringify(doc.metadata)}`);
+            }
+            console.log();
+        }
+    });
+    return kb;
+}
+//# sourceMappingURL=knowledge-base.js.map

package/dist/commands/knowledge-base.js.map

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package/dist/commands/literature.d.ts

@@ -0,0 +1,2 @@
+import { Command } from "commander";
+export declare function createLiteratureCommand(): Command;

package/dist/commands/literature.js

@@ -0,0 +1,302 @@
+import * as fs from "node:fs";
+import * as path from "node:path";
+import { RecursiveCharacterTextSplitter } from "@langchain/textsplitters";
+import cliProgress from "cli-progress";
+import { Command } from "commander";
+import { getModelConfig, getPdfDir, getProjectDataDir, getUserDataDir, getVectorStoreDir, } from "../config/index.js";
+import * as projectKb from "../db/project/knowledge-bases.js";
+import * as projectLit from "../db/project/literatures.js";
+import * as userKb from "../db/user/knowledge-bases.js";
+import * as userLit from "../db/user/literatures.js";
+import { extractPdfContent } from "../pdf/extractor.js";
+import { createVectorStore, loadVectorStore } from "../vector-store/index.js";
+function resolveKnowledgeBase(id) {
+    const pkb = projectKb.getKnowledgeBase(id);
+    if (pkb)
+        return { kb: pkb, scope: "project" };
+    const ukb = userKb.getKnowledgeBase(id);
+    if (ukb)
+        return { kb: ukb, scope: "user" };
+    return null;
+}
+function getBaseDir(scope) {
+    return scope === "project" ? getProjectDataDir() : getUserDataDir();
+}
+function getLitOps(scope) {
+    return scope === "project" ? projectLit : userLit;
+}
+export function createLiteratureCommand() {
+    const lit = new Command("lit").description("Manage literatures");
+    // ─── lit add ───────────────────────────────────────────────
+    lit
+        .command("add <knowledge-base-id> <pdf-path>")
+        .description("Add a literature from a PDF file")
+        .option("-t, --title <title>", "Literature title")
+        .action(async (kbId, pdfPath, options) => {
+        const resolved = resolveKnowledgeBase(kbId);
+        if (!resolved) {
+            console.error(`Knowledge base not found: ${kbId}`);
+            process.exit(1);
+        }
+        const { kb, scope } = resolved;
+        const baseDir = getBaseDir(scope);
+        const litOps = getLitOps(scope);
+        // Resolve PDF path
+        const absolutePdfPath = path.resolve(pdfPath);
+        if (!fs.existsSync(absolutePdfPath)) {
+            console.error(`PDF file not found: ${absolutePdfPath}`);
+            process.exit(1);
+        }
+        const title = options.title ?? path.basename(pdfPath, path.extname(pdfPath));
+        console.log(`Extracting PDF content...`);
+        const docs = await extractPdfContent(absolutePdfPath);
+        console.log(`  Extracted ${String(docs.length)} pages.`);
+        // Create literature record
+        const literature = litOps.createLiterature({
+            title,
+            titleTranslation: null,
+            author: null,
+            abstract: null,
+            summary: null,
+            keywords: [],
+            url: null,
+            notes: {},
+            knowledgeBaseId: kbId,
+        });
+        // Copy PDF to storage
+        const pdfDir = getPdfDir(baseDir);
+        fs.mkdirSync(pdfDir, { recursive: true });
+        fs.copyFileSync(absolutePdfPath, path.join(pdfDir, `${literature.id}.pdf`));
+        // Split text and add to vector store
+        console.log(`Splitting text...`);
+        const splitter = new RecursiveCharacterTextSplitter({
+            chunkSize: 1000,
+            chunkOverlap: 200,
+        });
+        const splitDocs = await splitter.splitDocuments(docs);
+        console.log(`  Created ${String(splitDocs.length)} chunks.`);
+        // Add literature ID metadata to each chunk
+        for (const doc of splitDocs) {
+            doc.metadata = { ...doc.metadata, literatureId: literature.id };
+        }
+        const vectorDir = path.join(getVectorStoreDir(baseDir), kbId);
+        const modelConfig = getModelConfig(kb.embeddingModelId);
+        console.log(`Embedding and storing vectors...`);
+        const bar = new cliProgress.SingleBar({}, cliProgress.Presets.shades_classic);
+        bar.start(splitDocs.length, 0);
+        // Check if vector store already exists
+        if (fs.existsSync(vectorDir)) {
+            const store = await loadVectorStore(modelConfig, vectorDir);
+            await store.addDocuments(splitDocs);
+            await store.save(vectorDir);
+        }
+        else {
+            fs.mkdirSync(vectorDir, { recursive: true });
+            await createVectorStore(splitDocs, modelConfig, vectorDir);
+        }
+        bar.update(splitDocs.length);
+        bar.stop();
+        console.log(`Literature added: ${literature.id}`);
+        console.log(`  Title: ${literature.title}`);
+    });
+    // ─── lit remove ────────────────────────────────────────────
+    lit
+        .command("remove <knowledge-base-id> <id>")
+        .description("Remove a literature")
+        .action((kbId, id) => {
+        const resolved = resolveKnowledgeBase(kbId);
+        if (!resolved) {
+            console.error(`Knowledge base not found: ${kbId}`);
+            process.exit(1);
+        }
+        const { scope } = resolved;
+        const baseDir = getBaseDir(scope);
+        const litOps = getLitOps(scope);
+        const literature = litOps.getLiterature(id);
+        if (!literature) {
+            console.error(`Literature not found: ${id}`);
+            process.exit(1);
+        }
+        // Delete PDF
+        const pdfPath = path.join(getPdfDir(baseDir), `${id}.pdf`);
+        if (fs.existsSync(pdfPath)) {
+            fs.unlinkSync(pdfPath);
+        }
+        // Delete literature record
+        litOps.deleteLiterature(id);
+        console.log(`Literature "${id}" removed.`);
+    });
+    // ─── lit update ────────────────────────────────────────────
+    lit
+        .command("update <knowledge-base-id> <id>")
+        .description("Update a literature")
+        .option("-t, --title <title>", "Title")
+        .option("--title-translation <translation>", "Title translation")
+        .option("-a, --author <author>", "Author")
+        .option("--abstract <abstract>", "Abstract")
+        .option("--summary <summary>", "Summary")
+        .option("--url <url>", "URL")
+        .option("--keywords <keywords>", "Keywords (comma-separated)")
+        .action((kbId, id, options) => {
+        const resolved = resolveKnowledgeBase(kbId);
+        if (!resolved) {
+            console.error(`Knowledge base not found: ${kbId}`);
+            process.exit(1);
+        }
+        const litOps = getLitOps(resolved.scope);
+        const input = {};
+        if (options.title !== undefined)
+            input["title"] = options.title;
+        if (options.titleTranslation !== undefined)
+            input["titleTranslation"] = options.titleTranslation;
+        if (options.author !== undefined)
+            input["author"] = options.author;
+        if (options.abstract !== undefined)
+            input["abstract"] = options.abstract;
+        if (options.summary !== undefined)
+            input["summary"] = options.summary;
+        if (options.url !== undefined)
+            input["url"] = options.url;
+        if (options.keywords !== undefined)
+            input["keywords"] = options.keywords.split(",").map((k) => k.trim());
+        const updated = litOps.updateLiterature(id, input);
+        if (!updated) {
+            console.error(`Literature not found: ${id}`);
+            process.exit(1);
+        }
+        console.log(`Literature "${id}" updated.`);
+    });
+    // ─── lit list ──────────────────────────────────────────────
+    lit
+        .command("list <knowledge-base-id>")
+        .description("List literatures in a knowledge base")
+        .action((kbId) => {
+        const resolved = resolveKnowledgeBase(kbId);
+        if (!resolved) {
+            console.error(`Knowledge base not found: ${kbId}`);
+            process.exit(1);
+        }
+        const litOps = getLitOps(resolved.scope);
+        const literatures = litOps.listLiteratures(kbId);
+        if (literatures.length === 0) {
+            console.log("No literatures found.");
+            return;
+        }
+        for (const l of literatures) {
+            console.log(`${l.id}`);
+            console.log(`  Title: ${l.title}`);
+            if (l.author)
+                console.log(`  Author: ${l.author}`);
+            console.log(`  Created: ${l.createdAt.toISOString()}`);
+            console.log();
+        }
+    });
+    // ─── lit show ──────────────────────────────────────────────
+    lit
+        .command("show <knowledge-base-id> <id>")
+        .description("Show literature details")
+        .action((kbId, id) => {
+        const resolved = resolveKnowledgeBase(kbId);
+        if (!resolved) {
+            console.error(`Knowledge base not found: ${kbId}`);
+            process.exit(1);
+        }
+        const litOps = getLitOps(resolved.scope);
+        const literature = litOps.getLiterature(id);
+        if (!literature) {
+            console.error(`Literature not found: ${id}`);
+            process.exit(1);
+        }
+        printLiterature(literature);
+    });
+    // ─── lit note ──────────────────────────────────────────────
+    const note = lit.command("note").description("Manage literature notes");
+    note
+        .command("list <literature-id>")
+        .description("List all notes for a literature")
+        .action((litId) => {
+        const literature = findLiterature(litId);
+        if (!literature) {
+            console.error(`Literature not found: ${litId}`);
+            process.exit(1);
+        }
+        const entries = Object.entries(literature.notes);
+        if (entries.length === 0) {
+            console.log("No notes found.");
+            return;
+        }
+        for (const [key, value] of entries) {
+            console.log(`${key}: ${value}`);
+        }
+    });
+    note
+        .command("set <literature-id> <key> <value>")
+        .description("Set a note on a literature")
+        .action((litId, key, value) => {
+        const found = findLiteratureWithScope(litId);
+        if (!found) {
+            console.error(`Literature not found: ${litId}`);
+            process.exit(1);
+        }
+        const litOps = getLitOps(found.scope);
+        const newNotes = { ...found.literature.notes, [key]: value };
+        litOps.updateLiterature(litId, { notes: newNotes });
+        console.log(`Note "${key}" set on literature "${litId}".`);
+    });
+    note
+        .command("remove <literature-id> <key>")
+        .description("Remove a note from a literature")
+        .action((litId, key) => {
+        const found = findLiteratureWithScope(litId);
+        if (!found) {
+            console.error(`Literature not found: ${litId}`);
+            process.exit(1);
+        }
+        const litOps = getLitOps(found.scope);
+        const newNotes = { ...found.literature.notes };
+        delete newNotes[key];
+        litOps.updateLiterature(litId, { notes: newNotes });
+        console.log(`Note "${key}" removed from literature "${litId}".`);
+    });
+    return lit;
+}
+// ─── Helpers ────────────────────────────────────────────────
+function findLiterature(id) {
+    return projectLit.getLiterature(id) ?? userLit.getLiterature(id);
+}
+function findLiteratureWithScope(id) {
+    const pLit = projectLit.getLiterature(id);
+    if (pLit)
+        return { literature: pLit, scope: "project" };
+    const uLit = userLit.getLiterature(id);
+    if (uLit)
+        return { literature: uLit, scope: "user" };
+    return null;
+}
+function printLiterature(lit) {
+    console.log(`ID: ${lit.id}`);
+    console.log(`Title: ${lit.title}`);
+    if (lit.titleTranslation)
+        console.log(`Title (translated): ${lit.titleTranslation}`);
+    if (lit.author)
+        console.log(`Author: ${lit.author}`);
+    if (lit.abstract)
+        console.log(`Abstract: ${lit.abstract}`);
+    if (lit.summary)
+        console.log(`Summary: ${lit.summary}`);
+    if (lit.keywords.length > 0)
+        console.log(`Keywords: ${lit.keywords.join(", ")}`);
+    if (lit.url)
+        console.log(`URL: ${lit.url}`);
+    console.log(`Knowledge Base: ${lit.knowledgeBaseId}`);
+    console.log(`Created: ${lit.createdAt.toISOString()}`);
+    console.log(`Updated: ${lit.updatedAt.toISOString()}`);
+    const noteEntries = Object.entries(lit.notes);
+    if (noteEntries.length > 0) {
+        console.log(`Notes:`);
+        for (const [key, value] of noteEntries) {
+            console.log(`  ${key}: ${value}`);
+        }
+    }
+}
+//# sourceMappingURL=literature.js.map