Bug: Bun and Deno fail to load JSON extension

[nisuxyz]

Kùzu version

v0.7.1

What operating system are you using?

Arch Linux

What happened?

When attempting to load the JSON extension by running the query

INSTALL json;
LOAD EXTENSION json;

It works when using node, but fails when using Bun or Deno:

» deno run -A src/lib/server/db/kuzu.ts                                                                                     
error: Uncaught (in promise) Error: IO exception: Failed to load library: /home/nisu/.kuzu/extension/0.7.1/linux_amd64/json/libjson.kuzu_extension which is needed by extension: json.
Error: /home/nisu/.kuzu/extension/0.7.1/linux_amd64/json/libjson.kuzu_extension: undefined symbol: _ZTVN4kuzu6common18BufferedSerializerE.

» bun run src/lib/server/db/kuzu.ts                                                                                         
error: IO exception: Failed to load library: /home/nisu/.kuzu/extension/0.7.1/linux_amd64/json/libjson.kuzu_extension which is needed by extension: json.
Error: /home/nisu/.kuzu/extension/0.7.1/linux_amd64/json/libjson.kuzu_extension: undefined symbol: _ZTVN4kuzu6common18BufferedSerializerE.

Bun v1.2.0 (Linux x64)

» node ./src/lib/server/db/kuzu.js                                                                                          
{
  db: Database {
    _database: NodeDatabase {},
    _isInitialized: true,
    _initPromise: null,
    _isClosed: false
  },
  conn: Connection {
    _database: Database {
      _database: NodeDatabase {},
      _isInitialized: true,
      _initPromise: null,
      _isClosed: false
    },
    _connection: NodeConnection {},
    _isInitialized: true,
    _initPromise: null,
    _isClosed: false
  }
}

I've checked that the file exists in the correct location. This is the code that's running:

import kuzu from 'kuzu';

const db = new kuzu.Database('./test_db');
const conn = new kuzu.Connection(db);

await conn.query(
	`INSTALL json;
LOAD EXTENSION json;`
);

console.log({ db, conn });

Are there known steps to reproduce?

No response

[acquamarin]

Hi @nisuxyz
Thanks for reporting to us, we will fix the issue soon

[acquamarin]

Hi @nisuxyz
I couldn't reproduce the bug on my machine.
Here is my step to reproduce:
For nodejs, i used:

const kuzu = require("kuzu");

(async () => {
  const db = new kuzu.Database("./test");
  const conn = new kuzu.Connection(db);
  await conn.query(
    "INSTALL json;"
  );
  await conn.query(
    "LOAD EXTENSION JSON;"
  );
})();

And run it as: node test.js

For deno:

import kuzu from "npm:kuzu";

const main = async () => {
  const db = new kuzu.Database("./test");
  const conn = new kuzu.Connection(db);

  await conn.query("INSTALL json;");
  await conn.query("LOAD EXTENSION JSON;");
};

main().catch((err) => {
  console.error("Error:", err);
});

For bun:

import kuzu from "kuzu";

(async () => {
  const db = new kuzu.Database("./test");
  const conn = new kuzu.Connection(db);

  // Create the tables
  await conn.query("INSTALL json;");
  await conn.query("LOAD EXTENSION JSON;");
})();

And run it as: bun run test_bun.test

BTW: Are you compiling the kuzu from source or use the npm package?

[nisuxyz]

I'm using the npm package, installed via bun. In order to properly install, installed with bun i kuzu and then bun pm trust kuzu. (In deno, installed with deno install --allow-scripts=npm:kuzu@0.7.1) I tested it on a separate ubuntu machine with a freshly installed bun/deno, with the same result for both, and it also was searching for uppercase JSON in the path when searching for the library:

/tmp/kuzu » cat /etc/os-release                                                                                                                                                
PRETTY_NAME="Ubuntu 22.04.5 LTS"
NAME="Ubuntu"
VERSION_ID="22.04"
VERSION="22.04.5 LTS (Jammy Jellyfish)"
VERSION_CODENAME=jammy
ID=ubuntu
ID_LIKE=debian
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
UBUNTU_CODENAME=jammy
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
/tmp/kuzu » ls ~/.kuzu                                                                                                                                                         
ls: cannot access '/home/nisu/.kuzu': No such file or directory
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
/tmp/kuzu » bun kuzu-load-json.ts                                                                                                                                                    
error: IO exception: Failed to load library: /home/nisu/.kuzu/extension/0.7.1/linux_amd64/JSON/libjson.kuzu_extension which is needed by extension: JSON.
Error: /home/nisu/.kuzu/extension/0.7.1/linux_amd64/JSON/libjson.kuzu_extension: cannot open shared object file: No such file or directory.

Bun v1.2.0 (Linux x64 baseline)
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
/tmp/kuzu » deno -A kuzu-load-json.ts                                                                                                                                            
error: Uncaught (in promise) Error: IO exception: Failed to load library: /home/nisu/.kuzu/extension/0.7.1/linux_amd64/JSON/libjson.kuzu_extension which is needed by extension: JSON.
Error: /home/nisu/.kuzu/extension/0.7.1/linux_amd64/JSON/libjson.kuzu_extension: cannot open shared object file: No such file or directory.
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
/tmp/kuzu » ls ~/.kuzu                                                                                                                                                           
extension
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
/tmp/kuzu » tree ~/.kuzu                                                                                                                                                             
/home/nisu/.kuzu
└── extension
    └── 0.7.1
        └── linux_amd64
            ├── common
            └── json
                └── libjson.kuzu_extension

5 directories, 1 file
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
/tmp/kuzu » mv ~/.kuzu/extension/0.7.1/linux_amd64/json ~/.kuzu/extension/0.7.1/linux_amd64/JSON

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
/tmp/kuzu » bun run kuzu-load-json.ts                                                                                                                                            
error: IO exception: Failed to load library: /home/nisu/.kuzu/extension/0.7.1/linux_amd64/JSON/libjson.kuzu_extension which is needed by extension: JSON.
Error: /home/nisu/.kuzu/extension/0.7.1/linux_amd64/JSON/libjson.kuzu_extension: undefined symbol: _ZTVN4kuzu6common18BufferedSerializerE.

Bun v1.2.0 (Linux x64 baseline)
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
/tmp/kuzu » deno -A kuzu-load-json.ts                                                                                                                                            
error: Uncaught (in promise) Error: IO exception: Failed to load library: /home/nisu/.kuzu/extension/0.7.1/linux_amd64/JSON/libjson.kuzu_extension which is needed by extension: JSON.
Error: /home/nisu/.kuzu/extension/0.7.1/linux_amd64/JSON/libjson.kuzu_extension: undefined symbol: _ZTVN4kuzu6common18BufferedSerializerE.

I tried with top level async as well as the wrapped function like your code:

// kuzu-load-json.ts
import kuzu from 'kuzu';

//const db = new kuzu.Database('./test');
//const conn = new kuzu.Connection(db);

//await conn.query('INSTALL json;');
//await conn.query('LOAD EXTENSION json;');

(async () => {
  const db = new kuzu.Database("./test");
  const conn = new kuzu.Connection(db);

  // Create the tables
  await conn.query("INSTALL json;");
  await conn.query("LOAD EXTENSION JSON;");
})();

[nisuxyz]

@acquamarin I tested on mac os 13.6.7 with

nisu@Nisus-MacBook-Pro-194:shell master ✗ 2h43m ◒ ⍉ ➜ clang --version
Apple clang version 15.0.0 (clang-1500.1.0.2.5)
Target: x86_64-apple-darwin22.6.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
nisu@Nisus-MacBook-Pro-194:shell master ✗ 2h43m ◒ ➜

I built and tested the CLI and hit a similar error, symbol not found, for a different symbol:

nisu@Nisus-MacBook-Pro-194:shell master ✗ 2h41m ◒ ⍉ ➜ ./kuzu
Opening the database under in-memory mode.
Enter ":help" for usage hints.
kuzu> INSTALL json;
┌─────────────────────────────────────┐
│ result                              │
│ STRING                              │
├─────────────────────────────────────┤
│ Extension: json has been installed. │
└─────────────────────────────────────┘
(1 tuple)
(1 column)
Time: 5.17ms (compiling), 336.79ms (executing)
kuzu> LOAD EXTENSION json;
Error: IO exception: Failed to load library: /Users/nisu/.kuzu/extension/0.7.0/osx_amd64/json/libjson.kuzu_extension which is needed by extension: json.
Error: dlopen(/Users/nisu/.kuzu/extension/0.7.0/osx_amd64/json/libjson.kuzu_extension, 0x0006): symbol not found in flat namespace '__ZN4kuzu4main13ClientContext16getMemoryManagerEv'.
kuzu>
nisu@Nisus-MacBook-Pro-194:shell master ✗ 2h45m ◒ ➜ ls ~/.kuzu/extension/0.7.0/osx_amd64/json/
libjson.kuzu_extension

I forgot to check out the 0.7.1 tag so I built the latest master branch, I will retry with 0.7.1 tag later tonight to see if the same thing happens