paper-manager 0.8.0 → 0.9.0

package/dist/config/init.test.js

@@ -1,61 +0,0 @@
-import * as fs from "node:fs";
-import * as path from "node:path";
-import { afterEach, beforeEach, describe, expect, it } from "vitest";
-import { getFilesDir, getProjectDataDir, getVectorStoreDir } from "./index.js";
-import { initScope } from "./init.js";
-// initScope() uses getProjectDataDir() which is a module-level constant resolved at import time.
-// This means process.chdir() cannot redirect it. We must clean up the actual project data dir
-// between tests to ensure isolation.
-let origCwd;
-beforeEach(() => {
-    origCwd = process.cwd();
-    const projectDir = getProjectDataDir();
-    if (fs.existsSync(projectDir)) {
-        fs.rmSync(projectDir, { recursive: true, force: true });
-    }
-});
-afterEach(() => {
-    process.chdir(origCwd);
-    const projectDir = getProjectDataDir();
-    if (fs.existsSync(projectDir)) {
-        fs.rmSync(projectDir, { recursive: true, force: true });
-    }
-});
-describe("initScope (project scope)", () => {
-    it("creates all expected files and directories on first run", () => {
-        const result = initScope();
-        const baseDir = result.baseDir;
-        // All items should be "created"
-        expect(result.items.every((item) => item.status === "created")).toBe(true);
-        expect(result.items).toHaveLength(5);
-        // Verify filesystem
-        expect(fs.existsSync(baseDir)).toBe(true);
-        expect(fs.existsSync(path.join(baseDir, "config.json"))).toBe(true);
-        expect(fs.existsSync(path.join(baseDir, "papers.db"))).toBe(true);
-        expect(fs.existsSync(getFilesDir(baseDir))).toBe(true);
-        expect(fs.existsSync(getVectorStoreDir(baseDir))).toBe(true);
-    });
-    it("config.json contains $schema field", () => {
-        const result = initScope();
-        const configContent = fs.readFileSync(path.join(result.baseDir, "config.json"), "utf-8");
-        const config = JSON.parse(configContent);
-        expect(config["$schema"]).toContain("config.schema.json");
-    });
-    it("is idempotent — second run reports all items as exists", () => {
-        initScope();
-        const result = initScope();
-        expect(result.items.every((item) => item.status === "exists")).toBe(true);
-        expect(result.items).toHaveLength(5);
-    });
-    it("preserves existing config.json content on second run", () => {
-        const result = initScope();
-        const configPath = path.join(result.baseDir, "config.json");
-        // Write custom content
-        fs.writeFileSync(configPath, JSON.stringify({ custom: "data" }));
-        // Second init should not overwrite
-        initScope();
-        const content = JSON.parse(fs.readFileSync(configPath, "utf-8"));
-        expect(content["custom"]).toBe("data");
-    });
-});
-//# sourceMappingURL=init.test.js.map

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

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package/dist/db/index.d.ts

@@ -1,7 +0,0 @@
-import type BetterSqlite3 from "better-sqlite3";
-import type { BetterSQLite3Database } from "drizzle-orm/better-sqlite3";
-export type AppDatabase = BetterSQLite3Database;
-export declare function openDatabase(dbPath: string): BetterSqlite3.Database;
-export declare function initializeDatabase(db: BetterSqlite3.Database): void;
-export declare function getUserDb(): AppDatabase;
-export declare function getProjectDb(): AppDatabase;

package/dist/db/index.js.map

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package/dist/db/index.test.d.ts

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

package/dist/db/index.test.js

@@ -1,32 +0,0 @@
-import { describe, expect, it } from "vitest";
-import { initializeDatabase, openDatabase } from "./index.js";
-// ─── openDatabase ────────────────────────────────────────────
-describe("openDatabase", () => {
-    it("opens an in-memory database with foreign keys enabled", () => {
-        const db = openDatabase(":memory:");
-        // WAL mode silently falls back to "memory" for in-memory databases
-        expect(db.pragma("foreign_keys", { simple: true })).toBe(1);
-        db.close();
-    });
-});
-// ─── initializeDatabase ──────────────────────────────────────
-describe("initializeDatabase", () => {
-    it("creates knowledge_bases and literatures tables", () => {
-        const db = openDatabase(":memory:");
-        initializeDatabase(db);
-        const tables = db
-            .prepare("SELECT name FROM sqlite_master WHERE type = 'table' ORDER BY name")
-            .all();
-        const tableNames = tables.map((t) => t.name);
-        expect(tableNames).toContain("knowledge_bases");
-        expect(tableNames).toContain("literatures");
-        db.close();
-    });
-    it("is idempotent — can be called multiple times", () => {
-        const db = openDatabase(":memory:");
-        initializeDatabase(db);
-        expect(() => initializeDatabase(db)).not.toThrow();
-        db.close();
-    });
-});
-//# sourceMappingURL=index.test.js.map

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

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package/dist/db/operations/knowledge-bases.d.ts

@@ -1,11 +0,0 @@
-import type { KnowledgeBaseMetadata, UpdateKnowledgeBaseInput } from "../../types/index.js";
-import type { AppDatabase } from "../index.js";
-export declare function createKnowledgeBase(db: AppDatabase, input: {
-    name: string;
-    description: string;
-    embeddingModelId: string;
-}): KnowledgeBaseMetadata;
-export declare function getKnowledgeBase(db: AppDatabase, id: string): KnowledgeBaseMetadata | null;
-export declare function listKnowledgeBases(db: AppDatabase): KnowledgeBaseMetadata[];
-export declare function updateKnowledgeBase(db: AppDatabase, id: string, input: UpdateKnowledgeBaseInput): KnowledgeBaseMetadata | null;
-export declare function deleteKnowledgeBase(db: AppDatabase, id: string): boolean;

package/dist/db/operations/knowledge-bases.js.map

@@ -1 +0,0 @@
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package/dist/db/operations/knowledge-bases.test.d.ts

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

package/dist/db/operations/knowledge-bases.test.js

@@ -1,71 +0,0 @@
-import { sql } from "drizzle-orm";
-import { beforeEach, describe, expect, it } from "vitest";
-import { createTestDb } from "../test-utils.js";
-import { createKnowledgeBase, deleteKnowledgeBase, getKnowledgeBase, listKnowledgeBases, } from "./knowledge-bases.js";
-let db;
-beforeEach(() => {
-    db = createTestDb();
-});
-const input = {
-    name: "Test KB",
-    description: "A test knowledge base",
-    embeddingModelId: "model-1",
-};
-// ─── createKnowledgeBase ─────────────────────────────────────
-describe("createKnowledgeBase", () => {
-    it("creates and returns a knowledge base with generated id and timestamps", () => {
-        const kb = createKnowledgeBase(db, input);
-        expect(kb.id).toMatch(/^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/);
-        expect(kb.name).toBe("Test KB");
-        expect(kb.description).toBe("A test knowledge base");
-        expect(kb.embeddingModelId).toBe("model-1");
-        expect(kb.createdAt).toBeInstanceOf(Date);
-        expect(kb.updatedAt).toBeInstanceOf(Date);
-    });
-    it("rejects duplicate names due to UNIQUE constraint", () => {
-        createKnowledgeBase(db, input);
-        expect(() => createKnowledgeBase(db, input)).toThrow();
-    });
-});
-// ─── getKnowledgeBase ────────────────────────────────────────
-describe("getKnowledgeBase", () => {
-    it("returns the knowledge base by id", () => {
-        const created = createKnowledgeBase(db, input);
-        const found = getKnowledgeBase(db, created.id);
-        expect(found).not.toBeNull();
-        expect(found.id).toBe(created.id);
-        expect(found.name).toBe("Test KB");
-    });
-    it("returns null for non-existent id", () => {
-        expect(getKnowledgeBase(db, "non-existent")).toBeNull();
-    });
-});
-// ─── listKnowledgeBases ──────────────────────────────────────
-describe("listKnowledgeBases", () => {
-    it("returns an empty array when no knowledge bases exist", () => {
-        expect(listKnowledgeBases(db)).toEqual([]);
-    });
-    it("returns knowledge bases ordered by created_at DESC", () => {
-        const kb1 = createKnowledgeBase(db, { ...input, name: "First" });
-        // Manually backdate kb1 so ordering is deterministic
-        db.run(sql `UPDATE knowledge_bases SET created_at = created_at - 1000 WHERE id = ${kb1.id}`);
-        const kb2 = createKnowledgeBase(db, { ...input, name: "Second" });
-        const list = listKnowledgeBases(db);
-        expect(list).toHaveLength(2);
-        // Second was created after First, so it should come first in DESC order
-        expect(list[0].id).toBe(kb2.id);
-        expect(list[1].id).toBe(kb1.id);
-    });
-});
-// ─── deleteKnowledgeBase ─────────────────────────────────────
-describe("deleteKnowledgeBase", () => {
-    it("deletes an existing knowledge base and returns true", () => {
-        const kb = createKnowledgeBase(db, input);
-        expect(deleteKnowledgeBase(db, kb.id)).toBe(true);
-        expect(getKnowledgeBase(db, kb.id)).toBeNull();
-    });
-    it("returns false for non-existent id", () => {
-        expect(deleteKnowledgeBase(db, "non-existent")).toBe(false);
-    });
-});
-//# sourceMappingURL=knowledge-bases.test.js.map

package/dist/db/operations/knowledge-bases.test.js.map

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package/dist/db/operations/literatures.d.ts

@@ -1,9 +0,0 @@
-import type { CreateLiteratureInput, LiteratureMetadata, UpdateLiteratureInput } from "../../types/index.js";
-import type { AppDatabase } from "../index.js";
-export declare function createLiterature(db: AppDatabase, input: CreateLiteratureInput): LiteratureMetadata;
-export declare function getLiterature(db: AppDatabase, id: string): LiteratureMetadata | null;
-export declare function listLiteratures(db: AppDatabase, knowledgeBaseId: string): LiteratureMetadata[];
-export declare function updateLiterature(db: AppDatabase, id: string, input: UpdateLiteratureInput): LiteratureMetadata | null;
-export declare function deleteLiterature(db: AppDatabase, id: string): boolean;
-export declare function deleteLiteraturesByKnowledgeBaseId(db: AppDatabase, knowledgeBaseId: string): number;
-export declare function getLiteraturesByKnowledgeBaseId(db: AppDatabase, knowledgeBaseId: string): LiteratureMetadata[];

package/dist/db/operations/literatures.js.map

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package/dist/db/operations/literatures.test.d.ts

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

package/dist/db/operations/literatures.test.js

@@ -1,156 +0,0 @@
-import { sql } from "drizzle-orm";
-import { beforeEach, describe, expect, it } from "vitest";
-import { createTestDb } from "../test-utils.js";
-import { createKnowledgeBase } from "./knowledge-bases.js";
-import { createLiterature, deleteLiterature, deleteLiteraturesByKnowledgeBaseId, getLiterature, listLiteratures, updateLiterature, } from "./literatures.js";
-let db;
-let kbId;
-beforeEach(() => {
-    db = createTestDb();
-    // Every literature needs a knowledge base
-    const kb = createKnowledgeBase(db, {
-        name: "Test KB",
-        description: "test",
-        embeddingModelId: "model-1",
-    });
-    kbId = kb.id;
-});
-function makeInput(overrides) {
-    return {
-        title: "A Paper",
-        titleTranslation: null,
-        author: "Alice",
-        abstract: "This paper explores...",
-        summary: null,
-        keywords: ["ai", "ml"],
-        url: null,
-        doi: null,
-        notes: { read: "yes" },
-        knowledgeBaseId: kbId,
-        ...overrides,
-    };
-}
-// ─── createLiterature ────────────────────────────────────────
-describe("createLiterature", () => {
-    it("creates a literature with generated id and timestamps", () => {
-        const lit = createLiterature(db, makeInput());
-        expect(lit.id).toMatch(/^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/);
-        expect(lit.title).toBe("A Paper");
-        expect(lit.author).toBe("Alice");
-        expect(lit.knowledgeBaseId).toBe(kbId);
-    });
-    it("round-trips JSON fields (keywords and notes)", () => {
-        const lit = createLiterature(db, makeInput({
-            keywords: ["deep learning", "transformer"],
-            notes: { chapter1: "interesting", chapter2: "review" },
-        }));
-        expect(lit.keywords).toEqual(["deep learning", "transformer"]);
-        expect(lit.notes).toEqual({ chapter1: "interesting", chapter2: "review" });
-    });
-    it("handles empty keywords and notes", () => {
-        const lit = createLiterature(db, makeInput({ keywords: [], notes: {} }));
-        expect(lit.keywords).toEqual([]);
-        expect(lit.notes).toEqual({});
-    });
-});
-// ─── getLiterature ───────────────────────────────────────────
-describe("getLiterature", () => {
-    it("returns the literature by id", () => {
-        const created = createLiterature(db, makeInput());
-        const found = getLiterature(db, created.id);
-        expect(found).not.toBeNull();
-        expect(found.title).toBe("A Paper");
-    });
-    it("returns null for non-existent id", () => {
-        expect(getLiterature(db, "non-existent")).toBeNull();
-    });
-});
-// ─── listLiteratures ─────────────────────────────────────────
-describe("listLiteratures", () => {
-    it("returns only literatures belonging to the given KB", () => {
-        const kb2 = createKnowledgeBase(db, {
-            name: "Other KB",
-            description: "other",
-            embeddingModelId: "model-1",
-        });
-        createLiterature(db, makeInput({ title: "Paper A" }));
-        createLiterature(db, makeInput({ title: "Paper B", knowledgeBaseId: kb2.id }));
-        const list = listLiteratures(db, kbId);
-        expect(list).toHaveLength(1);
-        expect(list[0].title).toBe("Paper A");
-    });
-    it("returns an empty array for a KB with no literatures", () => {
-        expect(listLiteratures(db, kbId)).toEqual([]);
-    });
-});
-// ─── updateLiterature ────────────────────────────────────────
-describe("updateLiterature", () => {
-    it("updates only the specified fields", () => {
-        const lit = createLiterature(db, makeInput());
-        const updated = updateLiterature(db, lit.id, { title: "New Title" });
-        expect(updated).not.toBeNull();
-        expect(updated.title).toBe("New Title");
-        // Other fields stay unchanged
-        expect(updated.author).toBe("Alice");
-        expect(updated.keywords).toEqual(["ai", "ml"]);
-    });
-    it("updates JSON fields correctly", () => {
-        const lit = createLiterature(db, makeInput());
-        const updated = updateLiterature(db, lit.id, {
-            keywords: ["new-tag"],
-            notes: { updated: "true" },
-        });
-        expect(updated.keywords).toEqual(["new-tag"]);
-        expect(updated.notes).toEqual({ updated: "true" });
-    });
-    it("advances updatedAt on update", () => {
-        const lit = createLiterature(db, makeInput());
-        const updated = updateLiterature(db, lit.id, { title: "Changed" });
-        expect(updated.updatedAt.getTime()).toBeGreaterThanOrEqual(lit.updatedAt.getTime());
-    });
-    it("returns the original when input is empty (no fields to update)", () => {
-        const lit = createLiterature(db, makeInput());
-        const unchanged = updateLiterature(db, lit.id, {});
-        expect(unchanged).not.toBeNull();
-        expect(unchanged.title).toBe(lit.title);
-        expect(unchanged.updatedAt.getTime()).toBe(lit.updatedAt.getTime());
-    });
-    it("returns null for non-existent id", () => {
-        expect(updateLiterature(db, "non-existent", { title: "X" })).toBeNull();
-    });
-});
-// ─── deleteLiterature ────────────────────────────────────────
-describe("deleteLiterature", () => {
-    it("deletes an existing literature and returns true", () => {
-        const lit = createLiterature(db, makeInput());
-        expect(deleteLiterature(db, lit.id)).toBe(true);
-        expect(getLiterature(db, lit.id)).toBeNull();
-    });
-    it("returns false for non-existent id", () => {
-        expect(deleteLiterature(db, "non-existent")).toBe(false);
-    });
-});
-// ─── deleteLiteraturesByKnowledgeBaseId ──────────────────────
-describe("deleteLiteraturesByKnowledgeBaseId", () => {
-    it("deletes all literatures in a KB and returns the count", () => {
-        createLiterature(db, makeInput({ title: "Paper 1" }));
-        createLiterature(db, makeInput({ title: "Paper 2" }));
-        expect(deleteLiteraturesByKnowledgeBaseId(db, kbId)).toBe(2);
-        expect(listLiteratures(db, kbId)).toEqual([]);
-    });
-    it("returns 0 when the KB has no literatures", () => {
-        expect(deleteLiteraturesByKnowledgeBaseId(db, kbId)).toBe(0);
-    });
-});
-// ─── Foreign Key Behavior ────────────────────────────────────
-describe("foreign key: ON DELETE SET NULL", () => {
-    it("sets knowledge_base_id to null when KB is deleted", () => {
-        const lit = createLiterature(db, makeInput());
-        // Delete the KB directly via SQL to trigger FK cascade
-        db.run(sql `DELETE FROM knowledge_bases WHERE id = ${kbId}`);
-        const raw = db.get(sql `SELECT knowledge_base_id FROM literatures WHERE id = ${lit.id}`);
-        expect(raw).toBeDefined();
-        expect(raw.knowledge_base_id).toBeNull();
-    });
-});
-//# sourceMappingURL=literatures.test.js.map

package/dist/db/operations/literatures.test.js.map

@@ -1 +0,0 @@
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package/dist/db/project/knowledge-bases.d.ts

@@ -1,10 +0,0 @@
-import type { KnowledgeBaseMetadata, UpdateKnowledgeBaseInput } from "../../types/index.js";
-export declare function createKnowledgeBase(input: {
-    name: string;
-    description: string;
-    embeddingModelId: string;
-}): KnowledgeBaseMetadata;
-export declare function getKnowledgeBase(id: string): KnowledgeBaseMetadata | null;
-export declare function listKnowledgeBases(): KnowledgeBaseMetadata[];
-export declare function updateKnowledgeBase(id: string, input: UpdateKnowledgeBaseInput): KnowledgeBaseMetadata | null;
-export declare function deleteKnowledgeBase(id: string): boolean;

package/dist/db/project/knowledge-bases.js.map

@@ -1 +0,0 @@
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package/dist/db/project/literatures.d.ts

@@ -1,8 +0,0 @@
-import type { CreateLiteratureInput, LiteratureMetadata, UpdateLiteratureInput } from "../../types/index.js";
-export declare function createLiterature(input: CreateLiteratureInput): LiteratureMetadata;
-export declare function getLiterature(id: string): LiteratureMetadata | null;
-export declare function listLiteratures(knowledgeBaseId: string): LiteratureMetadata[];
-export declare function updateLiterature(id: string, input: UpdateLiteratureInput): LiteratureMetadata | null;
-export declare function deleteLiterature(id: string): boolean;
-export declare function deleteLiteraturesByKnowledgeBaseId(knowledgeBaseId: string): number;
-export declare function getLiteraturesByKnowledgeBaseId(knowledgeBaseId: string): LiteratureMetadata[];

package/dist/db/project/literatures.js.map

@@ -1 +0,0 @@
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