paper-manager 0.4.2 → 0.6.0

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

@@ -1,25 +1,51 @@
 import * as crypto from "node:crypto";
-import { dbRowToKnowledgeBase } from "../index.js";
+import { desc, eq } from "drizzle-orm";
+import { knowledgeBases } from "../schema.js";
 export function createKnowledgeBase(db, input) {
     const id = crypto.randomUUID();
-    const now = Date.now();
-    db.prepare(`INSERT INTO knowledge_bases (id, name, description, embedding_model_id, created_at, updated_at)
-     VALUES (?, ?, ?, ?, ?, ?)`).run(id, input.name, input.description, input.embeddingModelId, now, now);
-    const row = db.prepare("SELECT * FROM knowledge_bases WHERE id = ?").get(id);
-    return dbRowToKnowledgeBase(row);
+    const now = new Date();
+    const row = db
+        .insert(knowledgeBases)
+        .values({
+        id,
+        name: input.name,
+        description: input.description,
+        embeddingModelId: input.embeddingModelId,
+        createdAt: now,
+        updatedAt: now,
+    })
+        .returning()
+        .get();
+    if (!row)
+        throw new Error("Failed to insert knowledge base");
+    return row;
 }
 export function getKnowledgeBase(db, id) {
-    const row = db.prepare("SELECT * FROM knowledge_bases WHERE id = ?").get(id);
-    if (!row)
-        return null;
-    return dbRowToKnowledgeBase(row);
+    const row = db.select().from(knowledgeBases).where(eq(knowledgeBases.id, id)).get();
+    return row ?? null;
 }
 export function listKnowledgeBases(db) {
-    const rows = db.prepare("SELECT * FROM knowledge_bases ORDER BY created_at DESC").all();
-    return rows.map(dbRowToKnowledgeBase);
+    return db.select().from(knowledgeBases).orderBy(desc(knowledgeBases.createdAt)).all();
+}
+export function updateKnowledgeBase(db, id, input) {
+    const updates = {};
+    if (input.name !== undefined)
+        updates.name = input.name;
+    if (input.description !== undefined)
+        updates.description = input.description;
+    if (Object.keys(updates).length === 0)
+        return getKnowledgeBase(db, id);
+    updates.updatedAt = new Date();
+    const row = db
+        .update(knowledgeBases)
+        .set(updates)
+        .where(eq(knowledgeBases.id, id))
+        .returning()
+        .get();
+    return row ?? null;
 }
 export function deleteKnowledgeBase(db, id) {
-    const result = db.prepare("DELETE FROM knowledge_bases WHERE id = ?").run(id);
+    const result = db.delete(knowledgeBases).where(eq(knowledgeBases.id, id)).run();
     return result.changes > 0;
 }
 //# sourceMappingURL=knowledge-bases.js.map

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

@@ -1 +1 @@
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package/dist/db/operations/knowledge-bases.test.js

@@ -1,13 +1,11 @@
-import { afterEach, beforeEach, describe, expect, it } from "vitest";
+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();
 });
-afterEach(() => {
-    db.close();
-});
 const input = {
     name: "Test KB",
     description: "A test knowledge base",
@@ -50,7 +48,7 @@ describe("listKnowledgeBases", () => {
     it("returns knowledge bases ordered by created_at DESC", () => {
         const kb1 = createKnowledgeBase(db, { ...input, name: "First" });
         // Manually backdate kb1 so ordering is deterministic
-        db.prepare("UPDATE knowledge_bases SET created_at = created_at - 1000 WHERE id = ?").run(kb1.id);
+        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);

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

@@ -1 +1 @@
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package/dist/db/operations/literatures.d.ts

@@ -1,9 +1,9 @@
-import type BetterSqlite3 from "better-sqlite3";
 import type { CreateLiteratureInput, LiteratureMetadata, UpdateLiteratureInput } from "../../types/index.js";
-export declare function createLiterature(db: BetterSqlite3.Database, input: CreateLiteratureInput): LiteratureMetadata;
-export declare function getLiterature(db: BetterSqlite3.Database, id: string): LiteratureMetadata | null;
-export declare function listLiteratures(db: BetterSqlite3.Database, knowledgeBaseId: string): LiteratureMetadata[];
-export declare function updateLiterature(db: BetterSqlite3.Database, id: string, input: UpdateLiteratureInput): LiteratureMetadata | null;
-export declare function deleteLiterature(db: BetterSqlite3.Database, id: string): boolean;
-export declare function deleteLiteraturesByKnowledgeBaseId(db: BetterSqlite3.Database, knowledgeBaseId: string): number;
-export declare function getLiteraturesByKnowledgeBaseId(db: BetterSqlite3.Database, knowledgeBaseId: string): LiteratureMetadata[];
+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

@@ -1,84 +1,81 @@
 import * as crypto from "node:crypto";
-import { dbRowToLiterature } from "../index.js";
+import { desc, eq } from "drizzle-orm";
+import { literatures } from "../schema.js";
 export function createLiterature(db, input) {
     const id = crypto.randomUUID();
-    const now = Date.now();
-    db.prepare(`INSERT INTO literatures (id, title, title_translation, author, abstract, summary, keywords, url, notes, knowledge_base_id, created_at, updated_at)
-     VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)`).run(id, input.title, input.titleTranslation ?? null, input.author ?? null, input.abstract ?? null, input.summary ?? null, JSON.stringify(input.keywords), input.url ?? null, JSON.stringify(input.notes), input.knowledgeBaseId, now, now);
-    const row = db.prepare("SELECT * FROM literatures WHERE id = ?").get(id);
-    return dbRowToLiterature(row);
+    const now = new Date();
+    const row = db
+        .insert(literatures)
+        .values({
+        id,
+        title: input.title,
+        titleTranslation: input.titleTranslation,
+        author: input.author,
+        abstract: input.abstract,
+        summary: input.summary,
+        keywords: input.keywords,
+        url: input.url,
+        doi: input.doi,
+        notes: input.notes,
+        knowledgeBaseId: input.knowledgeBaseId,
+        createdAt: now,
+        updatedAt: now,
+    })
+        .returning()
+        .get();
+    if (!row)
+        throw new Error("Failed to insert literature");
+    return row;
 }
 export function getLiterature(db, id) {
-    const row = db.prepare("SELECT * FROM literatures WHERE id = ?").get(id);
-    if (!row)
-        return null;
-    return dbRowToLiterature(row);
+    const row = db.select().from(literatures).where(eq(literatures.id, id)).get();
+    return row ?? null;
 }
 export function listLiteratures(db, knowledgeBaseId) {
-    const rows = db
-        .prepare("SELECT * FROM literatures WHERE knowledge_base_id = ? ORDER BY created_at DESC")
-        .all(knowledgeBaseId);
-    return rows.map(dbRowToLiterature);
+    return db
+        .select()
+        .from(literatures)
+        .where(eq(literatures.knowledgeBaseId, knowledgeBaseId))
+        .orderBy(desc(literatures.createdAt))
+        .all();
 }
 export function updateLiterature(db, id, input) {
-    const existing = getLiterature(db, id);
-    if (!existing)
-        return null;
-    const now = Date.now();
-    const fields = [];
-    const values = [];
-    if (input.title !== undefined) {
-        fields.push("title = ?");
-        values.push(input.title);
-    }
-    if (input.titleTranslation !== undefined) {
-        fields.push("title_translation = ?");
-        values.push(input.titleTranslation);
-    }
-    if (input.author !== undefined) {
-        fields.push("author = ?");
-        values.push(input.author);
-    }
-    if (input.abstract !== undefined) {
-        fields.push("abstract = ?");
-        values.push(input.abstract);
-    }
-    if (input.summary !== undefined) {
-        fields.push("summary = ?");
-        values.push(input.summary);
-    }
-    if (input.keywords !== undefined) {
-        fields.push("keywords = ?");
-        values.push(JSON.stringify(input.keywords));
-    }
-    if (input.url !== undefined) {
-        fields.push("url = ?");
-        values.push(input.url);
-    }
-    if (input.notes !== undefined) {
-        fields.push("notes = ?");
-        values.push(JSON.stringify(input.notes));
-    }
-    if (input.knowledgeBaseId !== undefined) {
-        fields.push("knowledge_base_id = ?");
-        values.push(input.knowledgeBaseId);
-    }
-    if (fields.length === 0)
-        return existing;
-    fields.push("updated_at = ?");
-    values.push(now);
-    values.push(id);
-    db.prepare(`UPDATE literatures SET ${fields.join(", ")} WHERE id = ?`).run(...values);
-    return getLiterature(db, id);
+    const updates = {};
+    if (input.title !== undefined)
+        updates.title = input.title;
+    if (input.titleTranslation !== undefined)
+        updates.titleTranslation = input.titleTranslation;
+    if (input.author !== undefined)
+        updates.author = input.author;
+    if (input.abstract !== undefined)
+        updates.abstract = input.abstract;
+    if (input.summary !== undefined)
+        updates.summary = input.summary;
+    if (input.keywords !== undefined)
+        updates.keywords = input.keywords;
+    if (input.url !== undefined)
+        updates.url = input.url;
+    if (input.doi !== undefined)
+        updates.doi = input.doi;
+    if (input.notes !== undefined)
+        updates.notes = input.notes;
+    if (input.knowledgeBaseId !== undefined)
+        updates.knowledgeBaseId = input.knowledgeBaseId;
+    if (Object.keys(updates).length === 0)
+        return getLiterature(db, id);
+    updates.updatedAt = new Date();
+    const row = db.update(literatures).set(updates).where(eq(literatures.id, id)).returning().get();
+    return row ?? null;
 }
 export function deleteLiterature(db, id) {
-    const result = db.prepare("DELETE FROM literatures WHERE id = ?").run(id);
+    const result = db.delete(literatures).where(eq(literatures.id, id)).run();
     return result.changes > 0;
 }
 export function deleteLiteraturesByKnowledgeBaseId(db, knowledgeBaseId) {
     const result = db
-        .prepare("DELETE FROM literatures WHERE knowledge_base_id = ?")
-        .run(knowledgeBaseId);
+        .delete(literatures)
+        .where(eq(literatures.knowledgeBaseId, knowledgeBaseId))
+        .run();
     return result.changes;
 }
 export function getLiteraturesByKnowledgeBaseId(db, knowledgeBaseId) {

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

@@ -1,4 +1,5 @@
-import { afterEach, beforeEach, describe, expect, it } from "vitest";
+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";
@@ -14,9 +15,6 @@ beforeEach(() => {
     });
     kbId = kb.id;
 });
-afterEach(() => {
-    db.close();
-});
 function makeInput(overrides) {
     return {
         title: "A Paper",
@@ -26,6 +24,7 @@ function makeInput(overrides) {
         summary: null,
         keywords: ["ai", "ml"],
         url: null,
+        doi: null,
         notes: { read: "yes" },
         knowledgeBaseId: kbId,
         ...overrides,
@@ -148,12 +147,10 @@ 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.prepare("DELETE FROM knowledge_bases WHERE id = ?").run(kbId);
-        // getLiterature() will throw because Zod schema requires knowledgeBaseId to be a UUID,
-        // but FK cascade sets it to NULL. Check the raw row instead.
-        const raw = db.prepare("SELECT knowledge_base_id FROM literatures WHERE id = ?").get(lit.id);
+        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();
+        expect(raw.knowledge_base_id).toBeNull();
     });
 });
 //# sourceMappingURL=literatures.test.js.map

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

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

@@ -1,4 +1,4 @@
-import type { KnowledgeBaseMetadata } from "../../types/index.js";
+import type { KnowledgeBaseMetadata, UpdateKnowledgeBaseInput } from "../../types/index.js";
 export declare function createKnowledgeBase(input: {
     name: string;
     description: string;
@@ -6,4 +6,5 @@ export declare function createKnowledgeBase(input: {
 }): 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

@@ -9,6 +9,9 @@ export function getKnowledgeBase(id) {
 export function listKnowledgeBases() {
     return ops.listKnowledgeBases(getProjectDb());
 }
+export function updateKnowledgeBase(id, input) {
+    return ops.updateKnowledgeBase(getProjectDb(), id, input);
+}
 export function deleteKnowledgeBase(id) {
     return ops.deleteKnowledgeBase(getProjectDb(), id);
 }

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

@@ -1 +1 @@
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+{"version":3,"file":"knowledge-bases.js","sourceRoot":"","sources":["../../../src/db/project/knowledge-bases.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAC3C,OAAO,KAAK,GAAG,MAAM,kCAAkC,CAAC;AAExD,MAAM,UAAU,mBAAmB,CAAC,KAInC;IACC,OAAO,GAAG,CAAC,mBAAmB,CAAC,YAAY,EAAE,EAAE,KAAK,CAAC,CAAC;AACxD,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,EAAU;IACzC,OAAO,GAAG,CAAC,gBAAgB,CAAC,YAAY,EAAE,EAAE,EAAE,CAAC,CAAC;AAClD,CAAC;AAED,MAAM,UAAU,kBAAkB;IAChC,OAAO,GAAG,CAAC,kBAAkB,CAAC,YAAY,EAAE,CAAC,CAAC;AAChD,CAAC;AAED,MAAM,UAAU,mBAAmB,CACjC,EAAU,EACV,KAA+B;IAE/B,OAAO,GAAG,CAAC,mBAAmB,CAAC,YAAY,EAAE,EAAE,EAAE,EAAE,KAAK,CAAC,CAAC;AAC5D,CAAC;AAED,MAAM,UAAU,mBAAmB,CAAC,EAAU;IAC5C,OAAO,GAAG,CAAC,mBAAmB,CAAC,YAAY,EAAE,EAAE,EAAE,CAAC,CAAC;AACrD,CAAC"}