diff --git a/py_hamt/__init__.py b/py_hamt/__init__.py index 40faa8f..5401546 100644 --- a/py_hamt/__init__.py +++ b/py_hamt/__init__.py @@ -1,5 +1,6 @@ from .hamt import HAMT, blake3_hashfn from .store import Store, DictStore, IPFSStore +from .zarr_encryption_transformer import create_zarr_encryption_transformers __all__ = [ "HAMT", @@ -7,4 +8,5 @@ "Store", "DictStore", "IPFSStore", + "create_zarr_encryption_transformers", ] diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index 2a8f2c4..8fb4533 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -6,7 +6,6 @@ import dag_cbor from dag_cbor.ipld import IPLDKind from multiformats import multihash - from .store import Store @@ -204,6 +203,11 @@ class HAMT(MutableMapping): You can modify the read status of a HAMT through the `make_read_only` or `enable_write` functions, so that the HAMT will block on making a change until all mutating operations are done. """ + transformer_encode: None | Callable[[str, bytes], bytes] + """This function is called to transform a value being inserted right before it gets sent to the Store.""" + transformer_decode: None | Callable[[str, bytes], bytes] + """This function is called to decode a value being retrieved after it is returned from the Store.""" + cache: dict[StoreID, Node] """@private""" max_cache_size_bytes: int @@ -250,6 +254,8 @@ def __init__( read_only: bool = False, root_node_id: IPLDKind = None, max_cache_size_bytes=10_000_000, # default to 10 megabytes + transformer_encode: None | Callable[[str, bytes], bytes] = None, + transformer_decode: None | Callable[[str, bytes], bytes] = None, ): self.store = store self.hash_fn = hash_fn @@ -261,6 +267,9 @@ def __init__( self.read_only = read_only self.lock = Lock() + self.transformer_encode = transformer_encode + self.transformer_decode = transformer_decode + if root_node_id is None: root_node = Node() self.root_node_id = self.write_node(root_node) @@ -340,7 +349,10 @@ def __setitem__(self, key_to_insert: str, val_to_insert: IPLDKind): if not self.read_only: self.lock.acquire(blocking=True) - val_ptr = self.store.save_raw(dag_cbor.encode(val_to_insert)) + val = dag_cbor.encode(val_to_insert) + if self.transformer_encode is not None: + val = self.transformer_encode(key_to_insert, val) + val_ptr = self.store.save_raw(val) node_stack: list[tuple[Link, Node]] = [] root_node = self.read_node(self.root_node_id) @@ -536,7 +548,10 @@ def __getitem__(self, key: str) -> IPLDKind: if not found_a_result: raise KeyError - return dag_cbor.decode(self.store.load(result_ptr)) + result_bytes = self.store.load(result_ptr) + if self.transformer_decode is not None: + result_bytes = self.transformer_decode(key, result_bytes) + return dag_cbor.decode(result_bytes) def __len__(self) -> int: key_count = 0 diff --git a/py_hamt/zarr_encryption_transformer.py b/py_hamt/zarr_encryption_transformer.py new file mode 100644 index 0000000..3266892 --- /dev/null +++ b/py_hamt/zarr_encryption_transformer.py @@ -0,0 +1,78 @@ +from typing import Callable +from pathlib import Path + + +import io + +from Crypto.Cipher import ChaCha20_Poly1305 +from Crypto.Random import get_random_bytes + + +# Metadata files to avoid encrypting (and decrypting) +encryption_exclude_files = [ + # top level meta data + ".zattrs", + ".zgroup", + ".zmetadata", + # found within variables, this includes .zattrs + ".zarray", + # important for coordinate variables, so that we can read bounds + "0", +] + +TransformerFN = Callable[[str, bytes], bytes] + + +def create_zarr_encryption_transformers( + encryption_key: bytes, + encrypted_vars: [str], +) -> tuple[TransformerFN, TransformerFN]: + """An encryption filter for ZARR data. + This class is serialized and stored along with the Zarr it is used with, so instead + of storing the encryption key, we store the hash of the encryption key, so it can be + looked up in the key registry at run time as needed. + Parameters + ---------- + key_hash: str + The hex digest of an encryption key. A key may be generated using + :func:`generate_encryption_key`. The hex digest is obtained by registering the + key using :func:`register_encryption_key`. + """ + + # codec_id = "xchacha20poly1305" + header = b"dClimate-Zarr" + + def _should_transform_key(key: str) -> bool: + if Path(key).name in encryption_exclude_files: + return False + return key.split("/")[0] in encrypted_vars + + def encode(key: str, val: bytes) -> bytes: + if not _should_transform_key(key): + return val + raw = io.BytesIO() + raw.write(val) + nonce = get_random_bytes(24) # XChaCha uses 24 byte (192 bit) nonce + cipher = ChaCha20_Poly1305.new(key=encryption_key, nonce=nonce) + cipher.update(header) + ciphertext, tag = cipher.encrypt_and_digest(raw.getbuffer()) + + return nonce + tag + ciphertext + + def decode(key: str, val: bytes): + if not _should_transform_key(key): + return val + + nonce, tag, ciphertext = val[:24], val[24:40], val[40:] + cipher = ChaCha20_Poly1305.new(key=encryption_key, nonce=nonce) + cipher.update(header) + plaintext = cipher.decrypt_and_verify(ciphertext, tag) + + # if out is not None: + # outbuf = io.BytesIO(plaintext) + # outbuf.readinto(out) + # return out + + return plaintext + + return encode, decode diff --git a/pyproject.toml b/pyproject.toml index a11dd6f..9d4ea6f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,6 +9,7 @@ dependencies = [ "msgspec>=0.18.6", "multiformats[full]>=0.3.1.post4", "requests>=2.32.3", + "pycryptodome", ] [build-system] @@ -26,6 +27,6 @@ dev = [ "snakeviz>=2.2.0", "pandas>=2.2.3", "numpy>=2.1.3", - "xarray>=2024.11.0", - "zarr>=2.18.3", + "xarray==2024.11.0", + "zarr==2.18.3", ] diff --git a/tests/test_zarr_encryption_ipfs.py b/tests/test_zarr_encryption_ipfs.py new file mode 100644 index 0000000..e7a4db2 --- /dev/null +++ b/tests/test_zarr_encryption_ipfs.py @@ -0,0 +1,173 @@ +import os +import shutil +import tempfile + +from multiformats import CID +import numpy as np +import pandas as pd +import xarray as xr +import pytest +import time + + +from Crypto.Random import get_random_bytes + +from py_hamt import HAMT, IPFSStore, create_zarr_encryption_transformers + + +@pytest.fixture +def random_zarr_dataset(): + """Creates a random xarray Dataset and saves it to a temporary zarr store. + + Returns: + tuple: (dataset_path, expected_data) + - dataset_path: Path to the zarr store + - expected_data: The original xarray Dataset for comparison + """ + # Create temporary directory for zarr store + temp_dir = tempfile.mkdtemp() + zarr_path = os.path.join(temp_dir, "test.zarr") + + # Coordinates of the random data + times = pd.date_range("2024-01-01", periods=100) + lats = np.linspace(-90, 90, 18) + lons = np.linspace(-180, 180, 36) + + # Create random variables with different shapes + temp = np.random.randn(len(times), len(lats), len(lons)) + precip = np.random.gamma(2, 0.5, size=(len(times), len(lats), len(lons))) + + # Create the dataset + ds = xr.Dataset( + { + "temp": ( + ["time", "lat", "lon"], + temp, + {"units": "celsius", "long_name": "Surface Temperature"}, + ), + "precip": ( + ["time", "lat", "lon"], + precip, + {"units": "mm/day", "long_name": "Daily Precipitation"}, + ), + }, + coords={ + "time": times, + "lat": ("lat", lats, {"units": "degrees_north"}), + "lon": ("lon", lons, {"units": "degrees_east"}), + }, + attrs={"description": "Test dataset with random weather data"}, + ) + + ds.to_zarr(zarr_path, mode="w") + + yield zarr_path, ds + + # Cleanup + shutil.rmtree(temp_dir) + + +def test_upload_then_read(random_zarr_dataset: tuple[str, xr.Dataset]): + zarr_path, expected_ds = random_zarr_dataset + test_ds = xr.open_zarr(zarr_path) + + # update precip and temp to have crypto: ["chacha"] + # TODO: THIS SHOULD BE DONE IN THE ZARRAY but it doesn't appear like xarray allows this + test_ds["precip"].attrs["crypto"] = ["xchacha20poly1305"] + test_ds["temp"].attrs["crypto"] = ["xchacha20poly1305"] + print("Writing this xarray Dataset to IPFS") + print(test_ds) + + start_time = time.time() + encryption_key = get_random_bytes(32) + + encode, decode = create_zarr_encryption_transformers( + encryption_key, ["temp", "precip"] + ) + hamt1 = HAMT( + store=IPFSStore(pin_on_add=False), + transformer_encode=encode, + transformer_decode=decode, + ) + test_ds.to_zarr(store=hamt1, mode="w") + + end_time = time.time() + total_time = end_time - start_time + print(f"Adding with encryption took {total_time:.2f} seconds") + + start_time = time.time() + hamt2 = HAMT( + store=IPFSStore(pin_on_add=False), + ) + test_ds.to_zarr(store=hamt2, mode="w") + end_time = time.time() + total_time = end_time - start_time + print(f"Adding without encryption took {total_time:.2f} seconds") + + hamt1_root: CID = hamt1.root_node_id # type: ignore + hamt2_root: CID = hamt2.root_node_id # type: ignore + print(f"No pin on add root CID: {hamt1_root}") + print(f"Pin on add root CID: {hamt2_root}") + + print("Reading in from IPFS") + hamt1_read = HAMT( + store=IPFSStore(), + root_node_id=hamt1_root, + read_only=True, + transformer_encode=encode, + transformer_decode=decode, + ) + hamt2_read = HAMT( + store=IPFSStore(), + root_node_id=hamt2_root, + read_only=True, + ) + start_time = time.time() + loaded_ds1 = xr.open_zarr(store=hamt1_read) + print(loaded_ds1) + loaded_ds2 = xr.open_zarr(store=hamt2_read) + end_time = time.time() + # Assert the values are the same + # Check if the values of 'temp' and 'precip' are equal in all datasets + assert np.array_equal(loaded_ds1["temp"].values, expected_ds["temp"].values), ( + "Temp values in loaded_ds1 and expected_ds are not identical!" + ) + assert np.array_equal(loaded_ds1["precip"].values, expected_ds["precip"].values), ( + "Precip values in loaded_ds1 and expected_ds are not identical!" + ) + assert np.array_equal(loaded_ds2["temp"].values, expected_ds["temp"].values), ( + "Temp values in loaded_ds2 and expected_ds are not identical!" + ) + assert np.array_equal(loaded_ds2["precip"].values, expected_ds["precip"].values), ( + "Precip values in loaded_ds2 and expected_ds are not identical!" + ) + # xr.testing.assert_identical(loaded_ds1, loaded_ds2) + # xr.testing.assert_identical(loaded_ds1, expected_ds) + total_time = (end_time - start_time) / 2 + print( + f"Took {total_time:.2f} seconds on average to load between the two loaded datasets" + ) + + # Test with no encryption key + + encrypted_no_transformer = HAMT( + store=IPFSStore(), + root_node_id=hamt1_root, + read_only=True, + ) + loaded_failure = xr.open_zarr(store=encrypted_no_transformer) + # Accessing data should raise an exception since we don't have the encryption key or the transformer + with pytest.raises(Exception): + loaded_failure["temp"].values + + assert "temp" in loaded_ds1 + assert "precip" in loaded_ds1 + assert loaded_ds1.temp.attrs["units"] == "celsius" + + assert loaded_ds1.temp.shape == expected_ds.temp.shape + + assert "temp" in loaded_ds2 + assert "precip" in loaded_ds2 + assert loaded_ds2.temp.attrs["units"] == "celsius" + + assert loaded_ds2.temp.shape == 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