manifest.py

import json
import re
from collections.abc import Iterable, Iterator
from typing import Any, Callable, Dict, NewType, Tuple, TypedDict, cast

import numpy as np
from pydantic import BaseModel, ConfigDict
from upath import UPath

from virtualizarr.types import ChunkKey

_INTEGER = (
    r"([1-9]+\d*|0)"  # matches 0 or an unsigned integer that does not begin with zero
)
_SEPARATOR = r"\."
_CHUNK_KEY = rf"^{_INTEGER}+({_SEPARATOR}{_INTEGER})*$"  # matches 1 integer, optionally followed by more integers each separated by a separator (i.e. a period)


class ChunkDictEntry(TypedDict):
    path: str
    offset: int
    length: int


ChunkDict = NewType("ChunkDict", dict[ChunkKey, ChunkDictEntry])


class ChunkEntry(BaseModel):
    """
    Information for a single chunk in the manifest.

    Stored in the form `{"path": "s3://bucket/foo.nc", "offset": 100, "length": 100}`.
    """

    model_config = ConfigDict(frozen=True)

    path: str  # TODO stricter typing/validation of possible local / remote paths?
    offset: int
    length: int

    def __repr__(self) -> str:
        return f"ChunkEntry(path='{self.path}', offset={self.offset}, length={self.length})"

    @classmethod
    def from_kerchunk(
        cls, path_and_byte_range_info: tuple[str] | tuple[str, int, int]
    ) -> "ChunkEntry":
        if len(path_and_byte_range_info) == 1:
            path = path_and_byte_range_info[0]
            offset = 0
            length = UPath(path).stat().st_size
        else:
            path, offset, length = path_and_byte_range_info
        return ChunkEntry(path=path, offset=offset, length=length)

    def to_kerchunk(self) -> tuple[str, int, int]:
        """Write out in the format that kerchunk uses for chunk entries."""
        return (self.path, self.offset, self.length)

    def dict(self) -> ChunkDictEntry:
        return ChunkDictEntry(path=self.path, offset=self.offset, length=self.length)


class ChunkManifest:
    """
    In-memory representation of a single Zarr chunk manifest.

    Stores the manifest internally as numpy arrays, so the most efficient way to create this object is via the `.from_arrays` constructor classmethod.

    The manifest can be converted to or from a dictionary which looks like this

        {
            "0.0.0": {"path": "s3://bucket/foo.nc", "offset": 100, "length": 100},
            "0.0.1": {"path": "s3://bucket/foo.nc", "offset": 200, "length": 100},
            "0.1.0": {"path": "s3://bucket/foo.nc", "offset": 300, "length": 100},
            "0.1.1": {"path": "s3://bucket/foo.nc", "offset": 400, "length": 100},
        }

    using the .__init__() and .dict() methods, so users of this class can think of the manifest as if it were a dict mapping zarr chunk keys to byte ranges.

    (See the chunk manifest SPEC proposal in https://github.com/zarr-developers/zarr-specs/issues/287.)

    Validation is done when this object is instantiated, and this class is immutable,
    so it's not possible to have a ChunkManifest object that does not represent a valid grid of chunks.
    """

    _paths: np.ndarray[Any, np.dtypes.StringDType]  # type: ignore[name-defined]
    _offsets: np.ndarray[Any, np.dtype[np.uint64]]
    _lengths: np.ndarray[Any, np.dtype[np.uint64]]

    def __init__(self, entries: dict) -> None:
        """
        Create a ChunkManifest from a dictionary mapping zarr chunk keys to byte ranges.

        Parameters
        ----------
        entries: dict
            Chunk keys and byte range information, as a dictionary of the form

                {
                    "0.0.0": {"path": "s3://bucket/foo.nc", "offset": 100, "length": 100},
                    "0.0.1": {"path": "s3://bucket/foo.nc", "offset": 200, "length": 100},
                    "0.1.0": {"path": "s3://bucket/foo.nc", "offset": 300, "length": 100},
                    "0.1.1": {"path": "s3://bucket/foo.nc", "offset": 400, "length": 100},
                }
        """

        # TODO do some input validation here first?
        validate_chunk_keys(entries.keys())

        # TODO should we actually optionally pass chunk grid shape in,
        # in case there are not enough chunks to give correct idea of full shape?
        shape = get_chunk_grid_shape(entries.keys())

        # Initializing to empty implies that entries with path='' are treated as missing chunks
        paths = np.empty(shape=shape, dtype=np.dtypes.StringDType())  # type: ignore[attr-defined]
        offsets = np.empty(shape=shape, dtype=np.dtype("uint64"))
        lengths = np.empty(shape=shape, dtype=np.dtype("uint64"))

        # populate the arrays
        for key, entry in entries.items():
            try:
                path, offset, length = entry.values()
                entry = ChunkEntry(path=path, offset=offset, length=length)
            except (ValueError, TypeError) as e:
                msg = (
                    "Each chunk entry must be of the form dict(path=<str>, offset=<int>, length=<int>), "
                    f"but got {entry}"
                )
                raise ValueError(msg) from e

            split_key = split(key)
            paths[split_key] = entry.path
            offsets[split_key] = entry.offset
            lengths[split_key] = entry.length

        self._paths = paths
        self._offsets = offsets
        self._lengths = lengths

    @classmethod
    def from_arrays(
        cls,
        paths: np.ndarray[Any, np.dtype[np.dtypes.StringDType]],  # type: ignore[name-defined]
        offsets: np.ndarray[Any, np.dtype[np.uint64]],
        lengths: np.ndarray[Any, np.dtype[np.uint64]],
    ) -> "ChunkManifest":
        """
        Create manifest directly from numpy arrays containing the path and byte range information.

        Useful if you want to avoid the memory overhead of creating an intermediate dictionary first,
        as these 3 arrays are what will be used internally to store the references.

        Parameters
        ----------
        paths: np.ndarray
        offsets: np.ndarray
        lengths: np.ndarray
        """

        # check types
        if not isinstance(paths, np.ndarray):
            raise TypeError(f"paths must be a numpy array, but got type {type(paths)}")
        if not isinstance(offsets, np.ndarray):
            raise TypeError(
                f"offsets must be a numpy array, but got type {type(offsets)}"
            )
        if not isinstance(lengths, np.ndarray):
            raise TypeError(
                f"lengths must be a numpy array, but got type {type(lengths)}"
            )

        # check dtypes
        if paths.dtype != np.dtypes.StringDType():  # type: ignore[attr-defined]
            raise ValueError(
                f"paths array must have a numpy variable-length string dtype, but got dtype {paths.dtype}"
            )
        if offsets.dtype != np.dtype("uint64"):
            raise ValueError(
                f"offsets array must have 64-bit unsigned integer dtype, but got dtype {offsets.dtype}"
            )
        if lengths.dtype != np.dtype("uint64"):
            raise ValueError(
                f"lengths array must have 64-bit unsigned integer dtype, but got dtype {lengths.dtype}"
            )

        # check shapes
        shape = paths.shape
        if offsets.shape != shape:
            raise ValueError(
                f"Shapes of the arrays must be consistent, but shapes of paths array and offsets array do not match: {paths.shape} vs {offsets.shape}"
            )
        if lengths.shape != shape:
            raise ValueError(
                f"Shapes of the arrays must be consistent, but shapes of paths array and lengths array do not match: {paths.shape} vs {lengths.shape}"
            )

        obj = object.__new__(cls)
        obj._paths = paths
        obj._offsets = offsets
        obj._lengths = lengths

        return obj

    @property
    def ndim_chunk_grid(self) -> int:
        """
        Number of dimensions in the chunk grid.

        Not the same as the dimension of an array backed by this chunk manifest.
        """
        return self._paths.ndim

    @property
    def shape_chunk_grid(self) -> tuple[int, ...]:
        """
        Number of separate chunks along each dimension.

        Not the same as the shape of an array backed by this chunk manifest.
        """
        return self._paths.shape

    def __repr__(self) -> str:
        return f"ChunkManifest<shape={self.shape_chunk_grid}>"

    def __getitem__(self, key: ChunkKey) -> ChunkEntry:
        indices = split(key)
        path = self._paths[indices]
        offset = self._offsets[indices]
        length = self._lengths[indices]
        return ChunkEntry(path=path, offset=offset, length=length)

    def __iter__(self) -> Iterator[ChunkKey]:
        # TODO make this work for numpy arrays
        raise NotImplementedError()
        # return iter(self._paths.keys())

    def __len__(self) -> int:
        return self._paths.size

    def dict(self) -> ChunkDict:
        """
        Convert the entire manifest to a nested dictionary.

        The returned dict will be of the form

        {
            "0.0.0": {"path": "s3://bucket/foo.nc", "offset": 100, "length": 100},
            "0.0.1": {"path": "s3://bucket/foo.nc", "offset": 200, "length": 100},
            "0.1.0": {"path": "s3://bucket/foo.nc", "offset": 300, "length": 100},
            "0.1.1": {"path": "s3://bucket/foo.nc", "offset": 400, "length": 100},
        }

        Entries whose path is an empty string will be interpreted as missing chunks and omitted from the dictionary.
        """

        coord_vectors = np.mgrid[
            tuple(slice(None, length) for length in self.shape_chunk_grid)
        ]

        d = {
            join(inds): dict(
                path=path.item(), offset=offset.item(), length=length.item()
            )
            for *inds, path, offset, length in np.nditer(
                [*coord_vectors, self._paths, self._offsets, self._lengths],
                flags=("refs_ok",),
            )
            if path.item() != ""  # don't include entry if path='' (i.e. empty chunk)
        }

        return cast(
            ChunkDict,
            d,
        )

    def __eq__(self, other: Any) -> bool:
        """Two manifests are equal if all of their entries are identical."""
        paths_equal = (self._paths == other._paths).all()
        offsets_equal = (self._offsets == other._offsets).all()
        lengths_equal = (self._lengths == other._lengths).all()
        return paths_equal and offsets_equal and lengths_equal

    @classmethod
    def from_zarr_json(cls, filepath: str) -> "ChunkManifest":
        """Create a ChunkManifest from a Zarr manifest.json file."""

        with open(filepath, "r") as manifest_file:
            entries = json.load(manifest_file)

        return cls(entries=entries)

    def to_zarr_json(self, filepath: str) -> None:
        """Write the manifest to a Zarr manifest.json file."""
        entries = self.dict()
        with open(filepath, "w") as json_file:
            json.dump(entries, json_file, indent=4, separators=(", ", ": "))

    @classmethod
    def _from_kerchunk_chunk_dict(
        cls,
        # The type hint requires `Dict` instead of `dict` due to
        # the conflicting ChunkManifest.dict method.
        kerchunk_chunk_dict: Dict[ChunkKey, str | tuple[str] | tuple[str, int, int]],
    ) -> "ChunkManifest":
        chunk_entries: dict[ChunkKey, ChunkDictEntry] = {}
        for k, v in kerchunk_chunk_dict.items():
            if isinstance(v, (str, bytes)):
                raise NotImplementedError("TODO: handle inlined data")
            elif not isinstance(v, (tuple, list)):
                raise TypeError(f"Unexpected type {type(v)} for chunk value: {v}")
            chunk_entries[k] = ChunkEntry.from_kerchunk(v).dict()
        return ChunkManifest(entries=chunk_entries)

    def rename_paths(
        self,
        new: str | Callable[[str], str],
    ) -> "ChunkManifest":
        """
        Rename paths to chunks in this manifest.

        Accepts either a string, in which case this new path will be used for all chunks, or
        a function which accepts the old path and returns the new path.

        Parameters
        ----------
        new
            New path to use for all chunks, either as a string, or as a function which accepts and returns strings.

        Returns
        -------
        manifest

        Examples
        --------
        Rename paths to reflect moving the referenced files from local storage to an S3 bucket.

        >>> def local_to_s3_url(old_local_path: str) -> str:
        ...     from pathlib import Path
        ...
        ...     new_s3_bucket_url = "http://s3.amazonaws.com/my_bucket/"
        ...
        ...     filename = Path(old_local_path).name
        ...     return str(new_s3_bucket_url / filename)

        >>> manifest.rename_paths(local_to_s3_url)

        See Also
        --------
        ManifestArray.rename_paths
        """
        if isinstance(new, str):
            renamed_paths = np.full_like(self._paths, fill_value=new)
        elif callable(new):
            vectorized_rename_fn = np.vectorize(new, otypes=[np.dtypes.StringDType()])  # type: ignore[attr-defined]
            renamed_paths = vectorized_rename_fn(self._paths)
        else:
            raise TypeError(
                f"Argument 'new' must be either a string or a callable that accepts and returns strings, but got type {type(new)}"
            )

        return self.from_arrays(
            paths=renamed_paths,
            offsets=self._offsets,
            lengths=self._lengths,
        )


def split(key: ChunkKey) -> Tuple[int, ...]:
    return tuple(int(i) for i in key.split("."))


def join(inds: Iterable[Any]) -> ChunkKey:
    return cast(ChunkKey, ".".join(str(i) for i in list(inds)))


def get_ndim_from_key(key: str) -> int:
    """Get number of dimensions implied by key, e.g. '4.5.6' -> 3"""
    return len(key.split("."))


def validate_chunk_keys(chunk_keys: Iterable[ChunkKey]):
    # Check if all keys have the correct form
    for key in chunk_keys:
        if not re.match(_CHUNK_KEY, key):
            raise ValueError(f"Invalid format for chunk key: '{key}'")

    # Check if all keys have the same number of dimensions
    first_key, *other_keys = list(chunk_keys)
    ndim = get_ndim_from_key(first_key)
    for key in other_keys:
        other_ndim = get_ndim_from_key(key)
        if other_ndim != ndim:
            raise ValueError(
                f"Inconsistent number of dimensions between chunk key {key} and {first_key}: {other_ndim} vs {ndim}"
            )


def get_chunk_grid_shape(chunk_keys: Iterable[ChunkKey]) -> tuple[int, ...]:
    # find max chunk index along each dimension
    zipped_indices = zip(*[split(key) for key in chunk_keys])
    chunk_grid_shape = tuple(
        max(indices_along_one_dim) + 1 for indices_along_one_dim in zipped_indices
    )
    return chunk_grid_shape