paper-manager 0.3.0 → 0.4.0

package/dist/ai/embed.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/ai/embed.test.js

@@ -0,0 +1,93 @@
+import { beforeEach, describe, expect, it, vi } from "vitest";
+// Mock the "ai" module before importing embed functions
+vi.mock("ai", () => ({
+    embed: vi.fn(),
+    embedMany: vi.fn(),
+}));
+// Mock the provider to avoid real OpenAI initialization
+vi.mock("./provider.js", () => ({
+    createEmbeddingModel: vi.fn(() => "mock-model"),
+}));
+// Import after mocks are set up
+const { embed: aiEmbed, embedMany: aiEmbedMany } = await import("ai");
+const { embed, embedMany } = await import("./embed.js");
+const baseConfig = {
+    id: "test",
+    provider: "openai",
+    model: "text-embedding-3-small",
+    apiKey: "sk-test",
+};
+beforeEach(() => {
+    vi.clearAllMocks();
+});
+// ─── embed ───────────────────────────────────────────────────
+describe("embed", () => {
+    it("calls ai embed and returns the embedding", async () => {
+        const mockEmbedding = [0.1, 0.2, 0.3];
+        aiEmbed.mockResolvedValue({ embedding: mockEmbedding });
+        const result = await embed(baseConfig, "hello");
+        expect(result).toEqual(mockEmbedding);
+        expect(aiEmbed).toHaveBeenCalledOnce();
+    });
+    it("passes providerOptions when dimensions is set", async () => {
+        aiEmbed.mockResolvedValue({ embedding: [0.1] });
+        await embed({ ...baseConfig, dimensions: 256 }, "hello");
+        expect(aiEmbed).toHaveBeenCalledWith(expect.objectContaining({
+            providerOptions: { openai: { dimensions: 256 } },
+        }));
+    });
+    it("passes undefined providerOptions when dimensions is not set", async () => {
+        aiEmbed.mockResolvedValue({ embedding: [0.1] });
+        await embed(baseConfig, "hello");
+        expect(aiEmbed).toHaveBeenCalledWith(expect.objectContaining({
+            providerOptions: undefined,
+        }));
+    });
+});
+// ─── embedMany ───────────────────────────────────────────────
+describe("embedMany", () => {
+    it("calls aiEmbedMany once when no batchSize is set", async () => {
+        const mockEmbeddings = [[0.1], [0.2], [0.3]];
+        aiEmbedMany.mockResolvedValue({ embeddings: mockEmbeddings });
+        const result = await embedMany(baseConfig, ["a", "b", "c"]);
+        expect(result).toEqual(mockEmbeddings);
+        expect(aiEmbedMany).toHaveBeenCalledOnce();
+    });
+    it("calls aiEmbedMany once when texts fit within batchSize", async () => {
+        const config = { ...baseConfig, batchSize: 5 };
+        aiEmbedMany.mockResolvedValue({ embeddings: [[0.1], [0.2]] });
+        const result = await embedMany(config, ["a", "b"]);
+        expect(result).toEqual([[0.1], [0.2]]);
+        expect(aiEmbedMany).toHaveBeenCalledOnce();
+    });
+    it("splits into batches when texts exceed batchSize", async () => {
+        const config = { ...baseConfig, batchSize: 2 };
+        aiEmbedMany
+            .mockResolvedValueOnce({ embeddings: [[0.1], [0.2]] })
+            .mockResolvedValueOnce({ embeddings: [[0.3], [0.4]] })
+            .mockResolvedValueOnce({ embeddings: [[0.5]] });
+        const result = await embedMany(config, ["a", "b", "c", "d", "e"]);
+        expect(result).toEqual([[0.1], [0.2], [0.3], [0.4], [0.5]]);
+        expect(aiEmbedMany).toHaveBeenCalledTimes(3);
+        // Verify batch contents
+        const calls = aiEmbedMany.mock.calls;
+        expect(calls[0][0]).toMatchObject({ values: ["a", "b"] });
+        expect(calls[1][0]).toMatchObject({ values: ["c", "d"] });
+        expect(calls[2][0]).toMatchObject({ values: ["e"] });
+    });
+    it("handles exact batchSize boundary without extra call", async () => {
+        const config = { ...baseConfig, batchSize: 2 };
+        aiEmbedMany
+            .mockResolvedValueOnce({ embeddings: [[0.1], [0.2]] })
+            .mockResolvedValueOnce({ embeddings: [[0.3], [0.4]] });
+        const result = await embedMany(config, ["a", "b", "c", "d"]);
+        expect(result).toEqual([[0.1], [0.2], [0.3], [0.4]]);
+        expect(aiEmbedMany).toHaveBeenCalledTimes(2);
+    });
+    it("handles empty input", async () => {
+        aiEmbedMany.mockResolvedValue({ embeddings: [] });
+        const result = await embedMany(baseConfig, []);
+        expect(result).toEqual([]);
+    });
+});
+//# sourceMappingURL=embed.test.js.map

package/dist/ai/embed.test.js.map

@@ -0,0 +1 @@
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package/dist/commands/knowledge-base.js

@@ -1,7 +1,7 @@
 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 { getConfig, getFilesDir, getModelConfig, 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";
@@ -94,12 +94,15 @@ export function createKnowledgeBaseCommand() {
         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, `${lit.id}.pdf`);
-            if (fs.existsSync(pdfPath)) {
-                fs.unlinkSync(pdfPath);
+        // 2. Delete stored files
+        const filesDir = getFilesDir(baseDir);
+        if (fs.existsSync(filesDir)) {
+            for (const lit of literatures) {
+                for (const entry of fs.readdirSync(filesDir, { withFileTypes: true })) {
+                    if (entry.isFile() && entry.name.startsWith(`${lit.id}.`)) {
+                        fs.unlinkSync(path.join(filesDir, entry.name));
+                    }
+                }
             }
         }
         // 3. Delete literatures from DB

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

@@ -1 +1 @@
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package/dist/commands/literature.js

@@ -4,13 +4,13 @@ import { RecursiveCharacterTextSplitter } from "@langchain/textsplitters";
 import chalk from "chalk";
 import cliProgress from "cli-progress";
 import { Command } from "commander";
-import { getModelConfig, getPdfDir, getProjectDataDir, getUserDataDir, getVectorStoreDir, } from "../config/index.js";
+import { getFilesDir, getModelConfig, 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 { extractContent } from "../extractor/index.js";
 import { log } from "../logger.js";
-import { extractPdfContent } from "../pdf/extractor.js";
 import { createVectorStore, loadVectorStore } from "../vector-store/index.js";
 function resolveKnowledgeBase(id) {
     const pkb = projectKb.getKnowledgeBase(id);
@@ -31,10 +31,10 @@ 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")
+        .command("add <knowledge-base-id> <lit-path>")
+        .description("Add a literature from a file (PDF, TXT, MD, TEX, etc.)")
         .option("-t, --title <title>", "Literature title")
-        .action(async (kbId, pdfPath, options) => {
+        .action(async (kbId, litPath, options) => {
         const resolved = resolveKnowledgeBase(kbId);
         if (!resolved) {
             log.error(`Knowledge base not found: ${kbId}`);
@@ -43,15 +43,15 @@ export function createLiteratureCommand() {
         const { kb, scope } = resolved;
         const baseDir = getBaseDir(scope);
         const litOps = getLitOps(scope);
-        // Resolve PDF path
-        const absolutePdfPath = path.resolve(pdfPath);
-        if (!fs.existsSync(absolutePdfPath)) {
-            log.error(`PDF file not found: ${absolutePdfPath}`);
+        // Resolve file path
+        const absolutePath = path.resolve(litPath);
+        if (!fs.existsSync(absolutePath)) {
+            log.error(`File not found: ${absolutePath}`);
             process.exit(1);
         }
-        const title = options.title ?? path.basename(pdfPath, path.extname(pdfPath));
-        log.info("Extracting PDF content...");
-        const docs = await extractPdfContent(absolutePdfPath);
+        const title = options.title ?? path.basename(litPath, path.extname(litPath));
+        log.info("Extracting content...");
+        const docs = await extractContent(absolutePath);
         log.step(`Extracted ${String(docs.length)} pages.`);
         // Create literature record
         const literature = litOps.createLiterature({
@@ -65,10 +65,11 @@ export function createLiteratureCommand() {
             notes: {},
             knowledgeBaseId: kbId,
         });
-        // Copy PDF to storage
-        const pdfDir = getPdfDir(baseDir);
-        fs.mkdirSync(pdfDir, { recursive: true });
-        fs.copyFileSync(absolutePdfPath, path.join(pdfDir, `${literature.id}.pdf`));
+        // Copy file to storage
+        const filesDir = getFilesDir(baseDir);
+        const ext = path.extname(litPath);
+        fs.mkdirSync(filesDir, { recursive: true });
+        fs.copyFileSync(absolutePath, path.join(filesDir, `${literature.id}${ext}`));
         // Split text and add to vector store
         log.info("Splitting text...");
         const splitter = new RecursiveCharacterTextSplitter({
@@ -86,8 +87,10 @@ export function createLiteratureCommand() {
         log.info("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)) {
+        // Check if both FAISS index files exist (not just the directory)
+        const hasIndex = fs.existsSync(path.join(vectorDir, "faiss.index")) &&
+            fs.existsSync(path.join(vectorDir, "docstore.json"));
+        if (hasIndex) {
             const store = await loadVectorStore(modelConfig, vectorDir);
             await store.addDocuments(splitDocs);
             await store.save(vectorDir);
@@ -119,10 +122,14 @@ export function createLiteratureCommand() {
             log.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 stored file (find by pattern <id>.*)
+        const filesDir = getFilesDir(baseDir);
+        if (fs.existsSync(filesDir)) {
+            for (const entry of fs.readdirSync(filesDir, { withFileTypes: true })) {
+                if (entry.isFile() && entry.name.startsWith(`${id}.`)) {
+                    fs.unlinkSync(path.join(filesDir, entry.name));
+                }
+            }
         }
         // Delete literature record
         litOps.deleteLiterature(id);

package/dist/commands/literature.js.map

@@ -1 +1 @@
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package/dist/config/index.d.ts

@@ -2,7 +2,7 @@ import * as z from "zod";
 import type { EmbeddingModelConfig } from "../types/index.js";
 export declare function getUserDataDir(): string;
 export declare function getProjectDataDir(): string;
-export declare function getPdfDir(base: string): string;
+export declare function getFilesDir(base: string): string;
 export declare function getVectorStoreDir(base: string): string;
 declare const configSchemas: {
     readonly embeddingModels: z.ZodRecord<z.ZodString, z.ZodObject<{

package/dist/config/index.js

@@ -12,8 +12,8 @@ export function getUserDataDir() {
 export function getProjectDataDir() {
     return PROJECT_DATA_DIR;
 }
-export function getPdfDir(base) {
-    return path.join(base, "pdfs");
+export function getFilesDir(base) {
+    return path.join(base, "files");
 }
 export function getVectorStoreDir(base) {
     return path.join(base, "vector-stores");

package/dist/config/index.js.map

@@ -1 +1 @@
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package/dist/config/index.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/config/index.test.js

@@ -0,0 +1,143 @@
+import * as fs from "node:fs";
+import * as os from "node:os";
+import * as path from "node:path";
+import { afterEach, beforeEach, describe, expect, it } from "vitest";
+import { getDefaultModelConfig, getFilesDir, getModelConfig, getVectorStoreDir, readConfigFile, writeConfigFile, } from "./index.js";
+// ─── Path Utilities ──────────────────────────────────────────
+describe("getFilesDir", () => {
+    it("appends files to base path", () => {
+        expect(getFilesDir("/data")).toBe(path.join("/data", "files"));
+    });
+});
+describe("getVectorStoreDir", () => {
+    it("appends vector-stores to base path", () => {
+        expect(getVectorStoreDir("/data")).toBe(path.join("/data", "vector-stores"));
+    });
+});
+// ─── Config File I/O ─────────────────────────────────────────
+describe("readConfigFile", () => {
+    let tmpDir;
+    beforeEach(() => {
+        tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), "paper-test-"));
+    });
+    afterEach(() => {
+        fs.rmSync(tmpDir, { recursive: true, force: true });
+    });
+    it("reads and parses a valid JSON config", () => {
+        const filePath = path.join(tmpDir, "config.json");
+        fs.writeFileSync(filePath, JSON.stringify({ key: "value" }));
+        expect(readConfigFile(filePath)).toEqual({ key: "value" });
+    });
+    it("returns empty object for non-existent file", () => {
+        expect(readConfigFile(path.join(tmpDir, "missing.json"))).toEqual({});
+    });
+    it("returns empty object for invalid JSON", () => {
+        const filePath = path.join(tmpDir, "bad.json");
+        fs.writeFileSync(filePath, "not json");
+        expect(readConfigFile(filePath)).toEqual({});
+    });
+    it("returns empty object when file contains a JSON array", () => {
+        const filePath = path.join(tmpDir, "array.json");
+        fs.writeFileSync(filePath, JSON.stringify([1, 2, 3]));
+        expect(readConfigFile(filePath)).toEqual({});
+    });
+});
+describe("writeConfigFile", () => {
+    let tmpDir;
+    beforeEach(() => {
+        tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), "paper-test-"));
+    });
+    afterEach(() => {
+        fs.rmSync(tmpDir, { recursive: true, force: true });
+    });
+    it("writes config as formatted JSON with trailing newline", () => {
+        const filePath = path.join(tmpDir, "config.json");
+        writeConfigFile(filePath, { hello: "world" });
+        const content = fs.readFileSync(filePath, "utf-8");
+        expect(content).toBe('{\n  "hello": "world"\n}\n');
+    });
+    it("creates parent directories if they do not exist", () => {
+        const filePath = path.join(tmpDir, "nested", "deep", "config.json");
+        writeConfigFile(filePath, { a: 1 });
+        expect(fs.existsSync(filePath)).toBe(true);
+    });
+});
+// ─── Config Access (requires real file system) ───────────────
+// These functions read from hardcoded user/project paths, so we test
+// the lower-level building blocks that don't depend on global state.
+describe("getConfig", () => {
+    let tmpDir;
+    let origHome;
+    let origCwd;
+    beforeEach(() => {
+        tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), "paper-test-"));
+        origHome = process.env["HOME"] ?? "";
+        origCwd = process.cwd();
+        // Point user/project config to temp dirs by monkey-patching env
+        // Note: getUserDataDir/getProjectDataDir read from module-level constants,
+        // so we write config files at the actual resolved paths instead.
+    });
+    afterEach(() => {
+        process.env["HOME"] = origHome;
+        process.chdir(origCwd);
+        fs.rmSync(tmpDir, { recursive: true, force: true });
+    });
+    it("validates and returns typed config values", () => {
+        // Test readConfigFile + schema validation directly
+        const filePath = path.join(tmpDir, "config.json");
+        const models = {
+            "model-1": {
+                provider: "openai",
+                model: "text-embedding-3-small",
+                apiKey: "sk-test",
+            },
+        };
+        writeConfigFile(filePath, { embeddingModels: models });
+        const config = readConfigFile(filePath);
+        expect(config["embeddingModels"]).toEqual(models);
+    });
+});
+// ─── setConfig / removeConfig / listConfig ───────────────────
+describe("setConfig / removeConfig / listConfig (via file path)", () => {
+    let tmpDir;
+    let filePath;
+    beforeEach(() => {
+        tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), "paper-test-"));
+        filePath = path.join(tmpDir, "config.json");
+        writeConfigFile(filePath, {});
+    });
+    afterEach(() => {
+        fs.rmSync(tmpDir, { recursive: true, force: true });
+    });
+    it("set then read round-trips a value", () => {
+        writeConfigFile(filePath, {});
+        const config = readConfigFile(filePath);
+        config["myKey"] = "myValue";
+        writeConfigFile(filePath, config);
+        const result = readConfigFile(filePath);
+        expect(result["myKey"]).toBe("myValue");
+    });
+    it("remove deletes a key", () => {
+        const config = { a: 1, b: 2 };
+        writeConfigFile(filePath, config);
+        delete config["a"];
+        writeConfigFile(filePath, config);
+        const result = readConfigFile(filePath);
+        expect(result["a"]).toBeUndefined();
+        expect(result["b"]).toBe(2);
+    });
+});
+// ─── getModelConfig / getDefaultModelConfig ──────────────────
+describe("getModelConfig / getDefaultModelConfig", () => {
+    // These depend on loadMergedConfig() which reads from fixed paths.
+    // We test the error paths which don't depend on file state.
+    it("getModelConfig throws when no models are configured", () => {
+        // loadMergedConfig returns {} when files don't exist,
+        // so getConfig("embeddingModels") returns null
+        expect(() => getModelConfig("nonexistent")).toThrow("No embedding models configured");
+    });
+    it("getDefaultModelConfig throws when no default is set", () => {
+        expect(() => getDefaultModelConfig()).toThrow("No default embedding model configured");
+    });
+});
+//# sourceMappingURL=index.test.js.map

package/dist/config/index.test.js.map

@@ -0,0 +1 @@
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package/dist/config/init.d.ts

@@ -2,7 +2,7 @@ export interface InitScopeResult {
     baseDir: string;
     items: Array<{
         name: string;
-        status: "created" | "exists";
+        status: "created" | "exists" | "migrated";
     }>;
 }
 export declare function initScope(options?: {

package/dist/config/init.js

@@ -1,7 +1,7 @@
 import * as fs from "node:fs";
 import * as path from "node:path";
 import { initializeDatabase, openDatabase } from "../db/index.js";
-import { getPdfDir, getProjectDataDir, getUserDataDir, getVectorStoreDir, writeConfigFile, } from "./index.js";
+import { getFilesDir, getProjectDataDir, getUserDataDir, getVectorStoreDir, writeConfigFile, } from "./index.js";
 export function initScope(options) {
     const baseDir = options?.user ? getUserDataDir() : getProjectDataDir();
     const items = [];
@@ -32,14 +32,31 @@ export function initScope(options) {
     initializeDatabase(db);
     db.close();
     items.push({ name: "papers.db", status: dbExisted ? "exists" : "created" });
-    // 4. pdfs/ directory
-    const pdfDir = getPdfDir(baseDir);
-    if (fs.existsSync(pdfDir)) {
-        items.push({ name: "pdfs/", status: "exists" });
+    // 4. files/ directory (with migration from pdfs/)
+    const filesDir = getFilesDir(baseDir);
+    const legacyPdfsDir = path.join(baseDir, "pdfs");
+    const legacyExists = fs.existsSync(legacyPdfsDir);
+    const filesExists = fs.existsSync(filesDir);
+    if (legacyExists && !filesExists) {
+        fs.renameSync(legacyPdfsDir, filesDir);
+        items.push({ name: "pdfs/ → files/", status: "migrated" });
+    }
+    else if (legacyExists && filesExists) {
+        for (const entry of fs.readdirSync(legacyPdfsDir, { withFileTypes: true })) {
+            const dest = path.join(filesDir, entry.name);
+            if (!fs.existsSync(dest)) {
+                fs.renameSync(path.join(legacyPdfsDir, entry.name), dest);
+            }
+        }
+        fs.rmSync(legacyPdfsDir, { recursive: true, force: true });
+        items.push({ name: "pdfs/ → files/", status: "migrated" });
+    }
+    else if (filesExists) {
+        items.push({ name: "files/", status: "exists" });
     }
     else {
-        fs.mkdirSync(pdfDir, { recursive: true });
-        items.push({ name: "pdfs/", status: "created" });
+        fs.mkdirSync(filesDir, { recursive: true });
+        items.push({ name: "files/", status: "created" });
     }
     // 5. vector-stores/ directory
     const vectorDir = getVectorStoreDir(baseDir);

package/dist/config/init.js.map

@@ -1 +1 @@
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package/dist/config/init.test.d.ts

@@ -0,0 +1 @@
+export {};