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1170 lines
43 KiB
1170 lines
43 KiB
5 months ago
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import base64
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import collections
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import io
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import itertools
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import logging
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import math
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import os
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from functools import lru_cache
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from typing import TYPE_CHECKING
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import fsspec.core
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try:
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import ujson as json
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except ImportError:
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if not TYPE_CHECKING:
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import json
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from ..asyn import AsyncFileSystem
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from ..callbacks import DEFAULT_CALLBACK
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from ..core import filesystem, open, split_protocol
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from ..utils import isfilelike, merge_offset_ranges, other_paths
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logger = logging.getLogger("fsspec.reference")
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class ReferenceNotReachable(RuntimeError):
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def __init__(self, reference, target, *args):
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super().__init__(*args)
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self.reference = reference
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self.target = target
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def __str__(self):
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return f'Reference "{self.reference}" failed to fetch target {self.target}'
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def _first(d):
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return list(d.values())[0]
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def _prot_in_references(path, references):
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ref = references.get(path)
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if isinstance(ref, (list, tuple)):
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return split_protocol(ref[0])[0] if ref[0] else ref[0]
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def _protocol_groups(paths, references):
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if isinstance(paths, str):
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return {_prot_in_references(paths, references): [paths]}
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out = {}
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for path in paths:
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protocol = _prot_in_references(path, references)
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out.setdefault(protocol, []).append(path)
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return out
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class RefsValuesView(collections.abc.ValuesView):
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def __iter__(self):
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for val in self._mapping.zmetadata.values():
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yield json.dumps(val).encode()
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yield from self._mapping._items.values()
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for field in self._mapping.listdir():
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chunk_sizes = self._mapping._get_chunk_sizes(field)
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if len(chunk_sizes) == 0:
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yield self._mapping[field + "/0"]
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continue
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yield from self._mapping._generate_all_records(field)
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class RefsItemsView(collections.abc.ItemsView):
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def __iter__(self):
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return zip(self._mapping.keys(), self._mapping.values())
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def ravel_multi_index(idx, sizes):
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val = 0
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mult = 1
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for i, s in zip(idx[::-1], sizes[::-1]):
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val += i * mult
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mult *= s
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return val
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class LazyReferenceMapper(collections.abc.MutableMapping):
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"""This interface can be used to read/write references from Parquet stores.
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It is not intended for other types of references.
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It can be used with Kerchunk's MultiZarrToZarr method to combine
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references into a parquet store.
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Examples of this use-case can be found here:
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https://fsspec.github.io/kerchunk/advanced.html?highlight=parquet#parquet-storage"""
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# import is class level to prevent numpy dep requirement for fsspec
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@property
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def np(self):
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import numpy as np
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return np
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@property
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def pd(self):
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import pandas as pd
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return pd
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def __init__(
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self, root, fs=None, out_root=None, cache_size=128, categorical_threshold=10
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):
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"""
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This instance will be writable, storing changes in memory until full partitions
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are accumulated or .flush() is called.
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To create an empty lazy store, use .create()
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Parameters
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----------
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root : str
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Root of parquet store
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fs : fsspec.AbstractFileSystem
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fsspec filesystem object, default is local filesystem.
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cache_size : int, default=128
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Maximum size of LRU cache, where cache_size*record_size denotes
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the total number of references that can be loaded in memory at once.
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categorical_threshold : int
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Encode urls as pandas.Categorical to reduce memory footprint if the ratio
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of the number of unique urls to total number of refs for each variable
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is greater than or equal to this number. (default 10)
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"""
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self.root = root
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self.chunk_sizes = {}
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self.out_root = out_root or self.root
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self.cat_thresh = categorical_threshold
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self.cache_size = cache_size
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self.dirs = None
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self.url = self.root + "/{field}/refs.{record}.parq"
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# TODO: derive fs from `root`
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self.fs = fsspec.filesystem("file") if fs is None else fs
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def __getattr__(self, item):
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if item in ("_items", "record_size", "zmetadata"):
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self.setup()
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# avoid possible recursion if setup fails somehow
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return self.__dict__[item]
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raise AttributeError(item)
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def setup(self):
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self._items = {}
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self._items[".zmetadata"] = self.fs.cat_file(
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"/".join([self.root, ".zmetadata"])
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)
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met = json.loads(self._items[".zmetadata"])
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self.record_size = met["record_size"]
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self.zmetadata = met["metadata"]
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# Define function to open and decompress refs
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@lru_cache(maxsize=self.cache_size)
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def open_refs(field, record):
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"""cached parquet file loader"""
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path = self.url.format(field=field, record=record)
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data = io.BytesIO(self.fs.cat_file(path))
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df = self.pd.read_parquet(data, engine="fastparquet")
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refs = {c: df[c].values for c in df.columns}
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return refs
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self.open_refs = open_refs
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@staticmethod
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def create(root, storage_options=None, fs=None, record_size=10000, **kwargs):
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"""Make empty parquet reference set
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First deletes the contents of the given directory, if it exists.
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Parameters
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----------
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root: str
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Directory to contain the output; will be created
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storage_options: dict | None
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For making the filesystem to use for writing is fs is None
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fs: FileSystem | None
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Filesystem for writing
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record_size: int
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Number of references per parquet file
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kwargs: passed to __init__
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Returns
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-------
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LazyReferenceMapper instance
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"""
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met = {"metadata": {}, "record_size": record_size}
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if fs is None:
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fs, root = fsspec.core.url_to_fs(root, **(storage_options or {}))
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if fs.exists(root):
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fs.rm(root, recursive=True)
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fs.makedirs(root, exist_ok=True)
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fs.pipe("/".join([root, ".zmetadata"]), json.dumps(met).encode())
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return LazyReferenceMapper(root, fs, **kwargs)
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def listdir(self, basename=True):
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"""List top-level directories"""
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# cache me?
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if self.dirs is None:
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dirs = [p.split("/", 1)[0] for p in self.zmetadata]
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self.dirs = {p for p in dirs if p and not p.startswith(".")}
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listing = self.dirs
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if basename:
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listing = [os.path.basename(path) for path in listing]
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return listing
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def ls(self, path="", detail=True):
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"""Shortcut file listings"""
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if not path:
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dirnames = self.listdir()
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others = set(
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[".zmetadata"]
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+ [name for name in self.zmetadata if "/" not in name]
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+ [name for name in self._items if "/" not in name]
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)
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if detail is False:
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others.update(dirnames)
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return sorted(others)
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dirinfo = [
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{"name": name, "type": "directory", "size": 0} for name in dirnames
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]
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fileinfo = [
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{
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"name": name,
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"type": "file",
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"size": len(
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json.dumps(self.zmetadata[name])
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if name in self.zmetadata
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else self._items[name]
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),
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}
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for name in others
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]
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return sorted(dirinfo + fileinfo, key=lambda s: s["name"])
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parts = path.split("/", 1)
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if len(parts) > 1:
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raise FileNotFoundError("Cannot list within directories right now")
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field = parts[0]
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others = set(
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[name for name in self.zmetadata if name.startswith(f"{path}/")]
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+ [name for name in self._items if name.startswith(f"{path}/")]
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)
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fileinfo = [
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{
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"name": name,
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"type": "file",
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"size": len(
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json.dumps(self.zmetadata[name])
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if name in self.zmetadata
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else self._items[name]
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),
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}
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for name in others
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]
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keys = self._keys_in_field(field)
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if detail is False:
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return list(others) + list(keys)
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recs = self._generate_all_records(field)
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recinfo = [
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{"name": name, "type": "file", "size": rec[-1]}
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for name, rec in zip(keys, recs)
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if rec[0] # filters out path==None, deleted/missing
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]
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return fileinfo + recinfo
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def _load_one_key(self, key):
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"""Get the reference for one key
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Returns bytes, one-element list or three-element list.
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"""
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if key in self._items:
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return self._items[key]
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elif key in self.zmetadata:
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return json.dumps(self.zmetadata[key]).encode()
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elif "/" not in key or self._is_meta(key):
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raise KeyError(key)
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field, _ = key.rsplit("/", 1)
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record, ri, chunk_size = self._key_to_record(key)
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maybe = self._items.get((field, record), {}).get(ri, False)
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if maybe is None:
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# explicitly deleted
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raise KeyError
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elif maybe:
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return maybe
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elif chunk_size == 0:
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return b""
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# Chunk keys can be loaded from row group and cached in LRU cache
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try:
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refs = self.open_refs(field, record)
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except (ValueError, TypeError, FileNotFoundError):
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raise KeyError(key)
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columns = ["path", "offset", "size", "raw"]
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selection = [refs[c][ri] if c in refs else None for c in columns]
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raw = selection[-1]
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if raw is not None:
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return raw
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|
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if selection[0] is None:
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raise KeyError("This reference does not exist or has been deleted")
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|
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if selection[1:3] == [0, 0]:
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# URL only
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return selection[:1]
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# URL, offset, size
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return selection[:3]
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|
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||
|
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@lru_cache(4096)
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|
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def _key_to_record(self, key):
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|
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"""Details needed to construct a reference for one key"""
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field, chunk = key.rsplit("/", 1)
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chunk_sizes = self._get_chunk_sizes(field)
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||
|
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if len(chunk_sizes) == 0:
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return 0, 0, 0
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||
|
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chunk_idx = [int(c) for c in chunk.split(".")]
|
||
|
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chunk_number = ravel_multi_index(chunk_idx, chunk_sizes)
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record = chunk_number // self.record_size
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ri = chunk_number % self.record_size
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||
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return record, ri, len(chunk_sizes)
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||
|
|
|
||
|
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def _get_chunk_sizes(self, field):
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|
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"""The number of chunks along each axis for a given field"""
|
||
|
|
if field not in self.chunk_sizes:
|
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zarray = self.zmetadata[f"{field}/.zarray"]
|
||
|
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size_ratio = [
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||
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math.ceil(s / c) for s, c in zip(zarray["shape"], zarray["chunks"])
|
||
|
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]
|
||
|
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self.chunk_sizes[field] = size_ratio or [1]
|
||
|
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return self.chunk_sizes[field]
|
||
|
|
|
||
|
|
def _generate_record(self, field, record):
|
||
|
|
"""The references for a given parquet file of a given field"""
|
||
|
|
refs = self.open_refs(field, record)
|
||
|
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it = iter(zip(*refs.values()))
|
||
|
|
if len(refs) == 3:
|
||
|
|
# All urls
|
||
|
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return (list(t) for t in it)
|
||
|
|
elif len(refs) == 1:
|
||
|
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# All raws
|
||
|
|
return refs["raw"]
|
||
|
|
else:
|
||
|
|
# Mix of urls and raws
|
||
|
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return (list(t[:3]) if not t[3] else t[3] for t in it)
|
||
|
|
|
||
|
|
def _generate_all_records(self, field):
|
||
|
|
"""Load all the references within a field by iterating over the parquet files"""
|
||
|
|
nrec = 1
|
||
|
|
for ch in self._get_chunk_sizes(field):
|
||
|
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nrec *= ch
|
||
|
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nrec = math.ceil(nrec / self.record_size)
|
||
|
|
for record in range(nrec):
|
||
|
|
yield from self._generate_record(field, record)
|
||
|
|
|
||
|
|
def values(self):
|
||
|
|
return RefsValuesView(self)
|
||
|
|
|
||
|
|
def items(self):
|
||
|
|
return RefsItemsView(self)
|
||
|
|
|
||
|
|
def __hash__(self):
|
||
|
|
return id(self)
|
||
|
|
|
||
|
|
def __getitem__(self, key):
|
||
|
|
return self._load_one_key(key)
|
||
|
|
|
||
|
|
def __setitem__(self, key, value):
|
||
|
|
if "/" in key and not self._is_meta(key):
|
||
|
|
field, chunk = key.rsplit("/", 1)
|
||
|
|
record, i, _ = self._key_to_record(key)
|
||
|
|
subdict = self._items.setdefault((field, record), {})
|
||
|
|
subdict[i] = value
|
||
|
|
if len(subdict) == self.record_size:
|
||
|
|
self.write(field, record)
|
||
|
|
else:
|
||
|
|
# metadata or top-level
|
||
|
|
self._items[key] = value
|
||
|
|
new_value = json.loads(
|
||
|
|
value.decode() if isinstance(value, bytes) else value
|
||
|
|
)
|
||
|
|
self.zmetadata[key] = {**self.zmetadata.get(key, {}), **new_value}
|
||
|
|
|
||
|
|
@staticmethod
|
||
|
|
def _is_meta(key):
|
||
|
|
return key.startswith(".z") or "/.z" in key
|
||
|
|
|
||
|
|
def __delitem__(self, key):
|
||
|
|
if key in self._items:
|
||
|
|
del self._items[key]
|
||
|
|
elif key in self.zmetadata:
|
||
|
|
del self.zmetadata[key]
|
||
|
|
else:
|
||
|
|
if "/" in key and not self._is_meta(key):
|
||
|
|
field, _ = key.rsplit("/", 1)
|
||
|
|
record, i, _ = self._key_to_record(key)
|
||
|
|
subdict = self._items.setdefault((field, record), {})
|
||
|
|
subdict[i] = None
|
||
|
|
if len(subdict) == self.record_size:
|
||
|
|
self.write(field, record)
|
||
|
|
else:
|
||
|
|
# metadata or top-level
|
||
|
|
self._items[key] = None
|
||
|
|
|
||
|
|
def write(self, field, record, base_url=None, storage_options=None):
|
||
|
|
# extra requirements if writing
|
||
|
|
import kerchunk.df
|
||
|
|
import numpy as np
|
||
|
|
import pandas as pd
|
||
|
|
|
||
|
|
partition = self._items[(field, record)]
|
||
|
|
original = False
|
||
|
|
if len(partition) < self.record_size:
|
||
|
|
try:
|
||
|
|
original = self.open_refs(field, record)
|
||
|
|
except IOError:
|
||
|
|
pass
|
||
|
|
|
||
|
|
if original:
|
||
|
|
paths = original["path"]
|
||
|
|
offsets = original["offset"]
|
||
|
|
sizes = original["size"]
|
||
|
|
raws = original["raw"]
|
||
|
|
else:
|
||
|
|
paths = np.full(self.record_size, np.nan, dtype="O")
|
||
|
|
offsets = np.zeros(self.record_size, dtype="int64")
|
||
|
|
sizes = np.zeros(self.record_size, dtype="int64")
|
||
|
|
raws = np.full(self.record_size, np.nan, dtype="O")
|
||
|
|
for j, data in partition.items():
|
||
|
|
if isinstance(data, list):
|
||
|
|
if (
|
||
|
|
str(paths.dtype) == "category"
|
||
|
|
and data[0] not in paths.dtype.categories
|
||
|
|
):
|
||
|
|
paths = paths.add_categories(data[0])
|
||
|
|
paths[j] = data[0]
|
||
|
|
if len(data) > 1:
|
||
|
|
offsets[j] = data[1]
|
||
|
|
sizes[j] = data[2]
|
||
|
|
elif data is None:
|
||
|
|
# delete
|
||
|
|
paths[j] = None
|
||
|
|
offsets[j] = 0
|
||
|
|
sizes[j] = 0
|
||
|
|
raws[j] = None
|
||
|
|
else:
|
||
|
|
# this is the only call into kerchunk, could remove
|
||
|
|
raws[j] = kerchunk.df._proc_raw(data)
|
||
|
|
# TODO: only save needed columns
|
||
|
|
df = pd.DataFrame(
|
||
|
|
{
|
||
|
|
"path": paths,
|
||
|
|
"offset": offsets,
|
||
|
|
"size": sizes,
|
||
|
|
"raw": raws,
|
||
|
|
},
|
||
|
|
copy=False,
|
||
|
|
)
|
||
|
|
if df.path.count() / (df.path.nunique() or 1) > self.cat_thresh:
|
||
|
|
df["path"] = df["path"].astype("category")
|
||
|
|
object_encoding = {"raw": "bytes", "path": "utf8"}
|
||
|
|
has_nulls = ["path", "raw"]
|
||
|
|
|
||
|
|
fn = f"{base_url or self.out_root}/{field}/refs.{record}.parq"
|
||
|
|
self.fs.mkdirs(f"{base_url or self.out_root}/{field}", exist_ok=True)
|
||
|
|
df.to_parquet(
|
||
|
|
fn,
|
||
|
|
engine="fastparquet",
|
||
|
|
storage_options=storage_options
|
||
|
|
or getattr(self.fs, "storage_options", None),
|
||
|
|
compression="zstd",
|
||
|
|
index=False,
|
||
|
|
stats=False,
|
||
|
|
object_encoding=object_encoding,
|
||
|
|
has_nulls=has_nulls,
|
||
|
|
# **kwargs,
|
||
|
|
)
|
||
|
|
partition.clear()
|
||
|
|
self._items.pop((field, record))
|
||
|
|
|
||
|
|
def flush(self, base_url=None, storage_options=None):
|
||
|
|
"""Output any modified or deleted keys
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
base_url: str
|
||
|
|
Location of the output
|
||
|
|
"""
|
||
|
|
# write what we have so far and clear sub chunks
|
||
|
|
for thing in list(self._items):
|
||
|
|
if isinstance(thing, tuple):
|
||
|
|
field, record = thing
|
||
|
|
self.write(
|
||
|
|
field,
|
||
|
|
record,
|
||
|
|
base_url=base_url,
|
||
|
|
storage_options=storage_options,
|
||
|
|
)
|
||
|
|
|
||
|
|
# gather .zmetadata from self._items and write that too
|
||
|
|
for k in list(self._items):
|
||
|
|
if k != ".zmetadata" and ".z" in k:
|
||
|
|
self.zmetadata[k] = json.loads(self._items.pop(k))
|
||
|
|
met = {"metadata": self.zmetadata, "record_size": self.record_size}
|
||
|
|
self._items[".zmetadata"] = json.dumps(met).encode()
|
||
|
|
self.fs.pipe(
|
||
|
|
"/".join([base_url or self.out_root, ".zmetadata"]),
|
||
|
|
self._items[".zmetadata"],
|
||
|
|
)
|
||
|
|
|
||
|
|
# TODO: only clear those that we wrote to?
|
||
|
|
self.open_refs.cache_clear()
|
||
|
|
|
||
|
|
def __len__(self):
|
||
|
|
# Caveat: This counts expected references, not actual - but is fast
|
||
|
|
count = 0
|
||
|
|
for field in self.listdir():
|
||
|
|
if field.startswith("."):
|
||
|
|
count += 1
|
||
|
|
else:
|
||
|
|
count += math.prod(self._get_chunk_sizes(field))
|
||
|
|
count += len(self.zmetadata) # all metadata keys
|
||
|
|
# any other files not in reference partitions
|
||
|
|
count += sum(1 for _ in self._items if not isinstance(_, tuple))
|
||
|
|
return count
|
||
|
|
|
||
|
|
def __iter__(self):
|
||
|
|
# Caveat: returns only existing keys, so the number of these does not
|
||
|
|
# match len(self)
|
||
|
|
metas = set(self.zmetadata)
|
||
|
|
metas.update(self._items)
|
||
|
|
for bit in metas:
|
||
|
|
if isinstance(bit, str):
|
||
|
|
yield bit
|
||
|
|
for field in self.listdir():
|
||
|
|
for k in self._keys_in_field(field):
|
||
|
|
if k in self:
|
||
|
|
yield k
|
||
|
|
|
||
|
|
def __contains__(self, item):
|
||
|
|
try:
|
||
|
|
self._load_one_key(item)
|
||
|
|
return True
|
||
|
|
except KeyError:
|
||
|
|
return False
|
||
|
|
|
||
|
|
def _keys_in_field(self, field):
|
||
|
|
"""List key names in given field
|
||
|
|
|
||
|
|
Produces strings like "field/x.y" appropriate from the chunking of the array
|
||
|
|
"""
|
||
|
|
chunk_sizes = self._get_chunk_sizes(field)
|
||
|
|
if len(chunk_sizes) == 0:
|
||
|
|
yield field + "/0"
|
||
|
|
return
|
||
|
|
inds = itertools.product(*(range(i) for i in chunk_sizes))
|
||
|
|
for ind in inds:
|
||
|
|
yield field + "/" + ".".join([str(c) for c in ind])
|
||
|
|
|
||
|
|
|
||
|
|
class ReferenceFileSystem(AsyncFileSystem):
|
||
|
|
"""View byte ranges of some other file as a file system
|
||
|
|
Initial version: single file system target, which must support
|
||
|
|
async, and must allow start and end args in _cat_file. Later versions
|
||
|
|
may allow multiple arbitrary URLs for the targets.
|
||
|
|
This FileSystem is read-only. It is designed to be used with async
|
||
|
|
targets (for now). This FileSystem only allows whole-file access, no
|
||
|
|
``open``. We do not get original file details from the target FS.
|
||
|
|
Configuration is by passing a dict of references at init, or a URL to
|
||
|
|
a JSON file containing the same; this dict
|
||
|
|
can also contain concrete data for some set of paths.
|
||
|
|
Reference dict format:
|
||
|
|
{path0: bytes_data, path1: (target_url, offset, size)}
|
||
|
|
https://github.com/fsspec/kerchunk/blob/main/README.md
|
||
|
|
"""
|
||
|
|
|
||
|
|
protocol = "reference"
|
||
|
|
|
||
|
|
def __init__(
|
||
|
|
self,
|
||
|
|
fo,
|
||
|
|
target=None,
|
||
|
|
ref_storage_args=None,
|
||
|
|
target_protocol=None,
|
||
|
|
target_options=None,
|
||
|
|
remote_protocol=None,
|
||
|
|
remote_options=None,
|
||
|
|
fs=None,
|
||
|
|
template_overrides=None,
|
||
|
|
simple_templates=True,
|
||
|
|
max_gap=64_000,
|
||
|
|
max_block=256_000_000,
|
||
|
|
cache_size=128,
|
||
|
|
**kwargs,
|
||
|
|
):
|
||
|
|
"""
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
fo : dict or str
|
||
|
|
The set of references to use for this instance, with a structure as above.
|
||
|
|
If str referencing a JSON file, will use fsspec.open, in conjunction
|
||
|
|
with target_options and target_protocol to open and parse JSON at this
|
||
|
|
location. If a directory, then assume references are a set of parquet
|
||
|
|
files to be loaded lazily.
|
||
|
|
target : str
|
||
|
|
For any references having target_url as None, this is the default file
|
||
|
|
target to use
|
||
|
|
ref_storage_args : dict
|
||
|
|
If references is a str, use these kwargs for loading the JSON file.
|
||
|
|
Deprecated: use target_options instead.
|
||
|
|
target_protocol : str
|
||
|
|
Used for loading the reference file, if it is a path. If None, protocol
|
||
|
|
will be derived from the given path
|
||
|
|
target_options : dict
|
||
|
|
Extra FS options for loading the reference file ``fo``, if given as a path
|
||
|
|
remote_protocol : str
|
||
|
|
The protocol of the filesystem on which the references will be evaluated
|
||
|
|
(unless fs is provided). If not given, will be derived from the first
|
||
|
|
URL that has a protocol in the templates or in the references, in that
|
||
|
|
order.
|
||
|
|
remote_options : dict
|
||
|
|
kwargs to go with remote_protocol
|
||
|
|
fs : AbstractFileSystem | dict(str, (AbstractFileSystem | dict))
|
||
|
|
Directly provide a file system(s):
|
||
|
|
- a single filesystem instance
|
||
|
|
- a dict of protocol:filesystem, where each value is either a filesystem
|
||
|
|
instance, or a dict of kwargs that can be used to create in
|
||
|
|
instance for the given protocol
|
||
|
|
|
||
|
|
If this is given, remote_options and remote_protocol are ignored.
|
||
|
|
template_overrides : dict
|
||
|
|
Swap out any templates in the references file with these - useful for
|
||
|
|
testing.
|
||
|
|
simple_templates: bool
|
||
|
|
Whether templates can be processed with simple replace (True) or if
|
||
|
|
jinja is needed (False, much slower). All reference sets produced by
|
||
|
|
``kerchunk`` are simple in this sense, but the spec allows for complex.
|
||
|
|
max_gap, max_block: int
|
||
|
|
For merging multiple concurrent requests to the same remote file.
|
||
|
|
Neighboring byte ranges will only be merged when their
|
||
|
|
inter-range gap is <= ``max_gap``. Default is 64KB. Set to 0
|
||
|
|
to only merge when it requires no extra bytes. Pass a negative
|
||
|
|
number to disable merging, appropriate for local target files.
|
||
|
|
Neighboring byte ranges will only be merged when the size of
|
||
|
|
the aggregated range is <= ``max_block``. Default is 256MB.
|
||
|
|
cache_size : int
|
||
|
|
Maximum size of LRU cache, where cache_size*record_size denotes
|
||
|
|
the total number of references that can be loaded in memory at once.
|
||
|
|
Only used for lazily loaded references.
|
||
|
|
kwargs : passed to parent class
|
||
|
|
"""
|
||
|
|
super().__init__(**kwargs)
|
||
|
|
self.target = target
|
||
|
|
self.template_overrides = template_overrides
|
||
|
|
self.simple_templates = simple_templates
|
||
|
|
self.templates = {}
|
||
|
|
self.fss = {}
|
||
|
|
self._dircache = {}
|
||
|
|
self.max_gap = max_gap
|
||
|
|
self.max_block = max_block
|
||
|
|
if isinstance(fo, str):
|
||
|
|
dic = dict(
|
||
|
|
**(ref_storage_args or target_options or {}), protocol=target_protocol
|
||
|
|
)
|
||
|
|
ref_fs, fo2 = fsspec.core.url_to_fs(fo, **dic)
|
||
|
|
if ref_fs.isfile(fo2):
|
||
|
|
# text JSON
|
||
|
|
with fsspec.open(fo, "rb", **dic) as f:
|
||
|
|
logger.info("Read reference from URL %s", fo)
|
||
|
|
text = json.load(f)
|
||
|
|
self._process_references(text, template_overrides)
|
||
|
|
else:
|
||
|
|
# Lazy parquet refs
|
||
|
|
logger.info("Open lazy reference dict from URL %s", fo)
|
||
|
|
self.references = LazyReferenceMapper(
|
||
|
|
fo2,
|
||
|
|
fs=ref_fs,
|
||
|
|
cache_size=cache_size,
|
||
|
|
)
|
||
|
|
else:
|
||
|
|
# dictionaries
|
||
|
|
self._process_references(fo, template_overrides)
|
||
|
|
if isinstance(fs, dict):
|
||
|
|
self.fss = {
|
||
|
|
k: (
|
||
|
|
fsspec.filesystem(k.split(":", 1)[0], **opts)
|
||
|
|
if isinstance(opts, dict)
|
||
|
|
else opts
|
||
|
|
)
|
||
|
|
for k, opts in fs.items()
|
||
|
|
}
|
||
|
|
if None not in self.fss:
|
||
|
|
self.fss[None] = filesystem("file")
|
||
|
|
return
|
||
|
|
if fs is not None:
|
||
|
|
# single remote FS
|
||
|
|
remote_protocol = (
|
||
|
|
fs.protocol[0] if isinstance(fs.protocol, tuple) else fs.protocol
|
||
|
|
)
|
||
|
|
self.fss[remote_protocol] = fs
|
||
|
|
|
||
|
|
if remote_protocol is None:
|
||
|
|
# get single protocol from any templates
|
||
|
|
for ref in self.templates.values():
|
||
|
|
if callable(ref):
|
||
|
|
ref = ref()
|
||
|
|
protocol, _ = fsspec.core.split_protocol(ref)
|
||
|
|
if protocol and protocol not in self.fss:
|
||
|
|
fs = filesystem(protocol, **(remote_options or {}))
|
||
|
|
self.fss[protocol] = fs
|
||
|
|
if remote_protocol is None:
|
||
|
|
# get single protocol from references
|
||
|
|
# TODO: warning here, since this can be very expensive?
|
||
|
|
for ref in self.references.values():
|
||
|
|
if callable(ref):
|
||
|
|
ref = ref()
|
||
|
|
if isinstance(ref, list) and ref[0]:
|
||
|
|
protocol, _ = fsspec.core.split_protocol(ref[0])
|
||
|
|
if protocol not in self.fss:
|
||
|
|
fs = filesystem(protocol, **(remote_options or {}))
|
||
|
|
self.fss[protocol] = fs
|
||
|
|
# only use first remote URL
|
||
|
|
break
|
||
|
|
|
||
|
|
if remote_protocol and remote_protocol not in self.fss:
|
||
|
|
fs = filesystem(remote_protocol, **(remote_options or {}))
|
||
|
|
self.fss[remote_protocol] = fs
|
||
|
|
|
||
|
|
self.fss[None] = fs or filesystem("file") # default one
|
||
|
|
|
||
|
|
def _cat_common(self, path, start=None, end=None):
|
||
|
|
path = self._strip_protocol(path)
|
||
|
|
logger.debug(f"cat: {path}")
|
||
|
|
try:
|
||
|
|
part = self.references[path]
|
||
|
|
except KeyError:
|
||
|
|
raise FileNotFoundError(path)
|
||
|
|
if isinstance(part, str):
|
||
|
|
part = part.encode()
|
||
|
|
if isinstance(part, bytes):
|
||
|
|
logger.debug(f"Reference: {path}, type bytes")
|
||
|
|
if part.startswith(b"base64:"):
|
||
|
|
part = base64.b64decode(part[7:])
|
||
|
|
return part, None, None
|
||
|
|
|
||
|
|
if len(part) == 1:
|
||
|
|
logger.debug(f"Reference: {path}, whole file => {part}")
|
||
|
|
url = part[0]
|
||
|
|
start1, end1 = start, end
|
||
|
|
else:
|
||
|
|
url, start0, size = part
|
||
|
|
logger.debug(f"Reference: {path} => {url}, offset {start0}, size {size}")
|
||
|
|
end0 = start0 + size
|
||
|
|
|
||
|
|
if start is not None:
|
||
|
|
if start >= 0:
|
||
|
|
start1 = start0 + start
|
||
|
|
else:
|
||
|
|
start1 = end0 + start
|
||
|
|
else:
|
||
|
|
start1 = start0
|
||
|
|
if end is not None:
|
||
|
|
if end >= 0:
|
||
|
|
end1 = start0 + end
|
||
|
|
else:
|
||
|
|
end1 = end0 + end
|
||
|
|
else:
|
||
|
|
end1 = end0
|
||
|
|
if url is None:
|
||
|
|
url = self.target
|
||
|
|
return url, start1, end1
|
||
|
|
|
||
|
|
async def _cat_file(self, path, start=None, end=None, **kwargs):
|
||
|
|
part_or_url, start0, end0 = self._cat_common(path, start=start, end=end)
|
||
|
|
if isinstance(part_or_url, bytes):
|
||
|
|
return part_or_url[start:end]
|
||
|
|
protocol, _ = split_protocol(part_or_url)
|
||
|
|
try:
|
||
|
|
await self.fss[protocol]._cat_file(part_or_url, start=start, end=end)
|
||
|
|
except Exception as e:
|
||
|
|
raise ReferenceNotReachable(path, part_or_url) from e
|
||
|
|
|
||
|
|
def cat_file(self, path, start=None, end=None, **kwargs):
|
||
|
|
part_or_url, start0, end0 = self._cat_common(path, start=start, end=end)
|
||
|
|
if isinstance(part_or_url, bytes):
|
||
|
|
return part_or_url[start:end]
|
||
|
|
protocol, _ = split_protocol(part_or_url)
|
||
|
|
try:
|
||
|
|
return self.fss[protocol].cat_file(part_or_url, start=start0, end=end0)
|
||
|
|
except Exception as e:
|
||
|
|
raise ReferenceNotReachable(path, part_or_url) from e
|
||
|
|
|
||
|
|
def pipe_file(self, path, value, **_):
|
||
|
|
"""Temporarily add binary data or reference as a file"""
|
||
|
|
self.references[path] = value
|
||
|
|
|
||
|
|
async def _get_file(self, rpath, lpath, **kwargs):
|
||
|
|
if self.isdir(rpath):
|
||
|
|
return os.makedirs(lpath, exist_ok=True)
|
||
|
|
data = await self._cat_file(rpath)
|
||
|
|
with open(lpath, "wb") as f:
|
||
|
|
f.write(data)
|
||
|
|
|
||
|
|
def get_file(self, rpath, lpath, callback=DEFAULT_CALLBACK, **kwargs):
|
||
|
|
if self.isdir(rpath):
|
||
|
|
return os.makedirs(lpath, exist_ok=True)
|
||
|
|
data = self.cat_file(rpath, **kwargs)
|
||
|
|
callback.set_size(len(data))
|
||
|
|
if isfilelike(lpath):
|
||
|
|
lpath.write(data)
|
||
|
|
else:
|
||
|
|
with open(lpath, "wb") as f:
|
||
|
|
f.write(data)
|
||
|
|
callback.absolute_update(len(data))
|
||
|
|
|
||
|
|
def get(self, rpath, lpath, recursive=False, **kwargs):
|
||
|
|
if recursive:
|
||
|
|
# trigger directory build
|
||
|
|
self.ls("")
|
||
|
|
rpath = self.expand_path(rpath, recursive=recursive)
|
||
|
|
fs = fsspec.filesystem("file", auto_mkdir=True)
|
||
|
|
targets = other_paths(rpath, lpath)
|
||
|
|
if recursive:
|
||
|
|
data = self.cat([r for r in rpath if not self.isdir(r)])
|
||
|
|
else:
|
||
|
|
data = self.cat(rpath)
|
||
|
|
for remote, local in zip(rpath, targets):
|
||
|
|
if remote in data:
|
||
|
|
fs.pipe_file(local, data[remote])
|
||
|
|
|
||
|
|
def cat(self, path, recursive=False, on_error="raise", **kwargs):
|
||
|
|
if isinstance(path, str) and recursive:
|
||
|
|
raise NotImplementedError
|
||
|
|
if isinstance(path, list) and (recursive or any("*" in p for p in path)):
|
||
|
|
raise NotImplementedError
|
||
|
|
# TODO: if references is lazy, pre-fetch all paths in batch before access
|
||
|
|
proto_dict = _protocol_groups(path, self.references)
|
||
|
|
out = {}
|
||
|
|
for proto, paths in proto_dict.items():
|
||
|
|
fs = self.fss[proto]
|
||
|
|
urls, starts, ends, valid_paths = [], [], [], []
|
||
|
|
for p in paths:
|
||
|
|
# find references or label not-found. Early exit if any not
|
||
|
|
# found and on_error is "raise"
|
||
|
|
try:
|
||
|
|
u, s, e = self._cat_common(p)
|
||
|
|
except FileNotFoundError as err:
|
||
|
|
if on_error == "raise":
|
||
|
|
raise
|
||
|
|
if on_error != "omit":
|
||
|
|
out[p] = err
|
||
|
|
else:
|
||
|
|
urls.append(u)
|
||
|
|
starts.append(s)
|
||
|
|
ends.append(e)
|
||
|
|
valid_paths.append(p)
|
||
|
|
|
||
|
|
# process references into form for merging
|
||
|
|
urls2 = []
|
||
|
|
starts2 = []
|
||
|
|
ends2 = []
|
||
|
|
paths2 = []
|
||
|
|
whole_files = set()
|
||
|
|
for u, s, e, p in zip(urls, starts, ends, valid_paths):
|
||
|
|
if isinstance(u, bytes):
|
||
|
|
# data
|
||
|
|
out[p] = u
|
||
|
|
elif s is None:
|
||
|
|
# whole file - limits are None, None, but no further
|
||
|
|
# entries take for this file
|
||
|
|
whole_files.add(u)
|
||
|
|
urls2.append(u)
|
||
|
|
starts2.append(s)
|
||
|
|
ends2.append(e)
|
||
|
|
paths2.append(p)
|
||
|
|
for u, s, e, p in zip(urls, starts, ends, valid_paths):
|
||
|
|
# second run to account for files that are to be loaded whole
|
||
|
|
if s is not None and u not in whole_files:
|
||
|
|
urls2.append(u)
|
||
|
|
starts2.append(s)
|
||
|
|
ends2.append(e)
|
||
|
|
paths2.append(p)
|
||
|
|
|
||
|
|
# merge and fetch consolidated ranges
|
||
|
|
new_paths, new_starts, new_ends = merge_offset_ranges(
|
||
|
|
list(urls2),
|
||
|
|
list(starts2),
|
||
|
|
list(ends2),
|
||
|
|
sort=True,
|
||
|
|
max_gap=self.max_gap,
|
||
|
|
max_block=self.max_block,
|
||
|
|
)
|
||
|
|
bytes_out = fs.cat_ranges(new_paths, new_starts, new_ends)
|
||
|
|
|
||
|
|
# unbundle from merged bytes - simple approach
|
||
|
|
for u, s, e, p in zip(urls, starts, ends, valid_paths):
|
||
|
|
if p in out:
|
||
|
|
continue # was bytes, already handled
|
||
|
|
for np, ns, ne, b in zip(new_paths, new_starts, new_ends, bytes_out):
|
||
|
|
if np == u and (ns is None or ne is None):
|
||
|
|
if isinstance(b, Exception):
|
||
|
|
out[p] = b
|
||
|
|
else:
|
||
|
|
out[p] = b[s:e]
|
||
|
|
elif np == u and s >= ns and e <= ne:
|
||
|
|
if isinstance(b, Exception):
|
||
|
|
out[p] = b
|
||
|
|
else:
|
||
|
|
out[p] = b[s - ns : (e - ne) or None]
|
||
|
|
|
||
|
|
for k, v in out.copy().items():
|
||
|
|
# these were valid references, but fetch failed, so transform exc
|
||
|
|
if isinstance(v, Exception) and k in self.references:
|
||
|
|
ex = out[k]
|
||
|
|
new_ex = ReferenceNotReachable(k, self.references[k])
|
||
|
|
new_ex.__cause__ = ex
|
||
|
|
if on_error == "raise":
|
||
|
|
raise new_ex
|
||
|
|
elif on_error != "omit":
|
||
|
|
out[k] = new_ex
|
||
|
|
|
||
|
|
if len(out) == 1 and isinstance(path, str) and "*" not in path:
|
||
|
|
return _first(out)
|
||
|
|
return out
|
||
|
|
|
||
|
|
def _process_references(self, references, template_overrides=None):
|
||
|
|
vers = references.get("version", None)
|
||
|
|
if vers is None:
|
||
|
|
self._process_references0(references)
|
||
|
|
elif vers == 1:
|
||
|
|
self._process_references1(references, template_overrides=template_overrides)
|
||
|
|
else:
|
||
|
|
raise ValueError(f"Unknown reference spec version: {vers}")
|
||
|
|
# TODO: we make dircache by iterating over all entries, but for Spec >= 1,
|
||
|
|
# can replace with programmatic. Is it even needed for mapper interface?
|
||
|
|
|
||
|
|
def _process_references0(self, references):
|
||
|
|
"""Make reference dict for Spec Version 0"""
|
||
|
|
if isinstance(references, dict):
|
||
|
|
# do not do this for lazy/parquet backend, which will not make dicts,
|
||
|
|
# but must remain writable in the original object
|
||
|
|
references = {
|
||
|
|
key: json.dumps(val) if isinstance(val, dict) else val
|
||
|
|
for key, val in references.items()
|
||
|
|
}
|
||
|
|
self.references = references
|
||
|
|
|
||
|
|
def _process_references1(self, references, template_overrides=None):
|
||
|
|
if not self.simple_templates or self.templates:
|
||
|
|
import jinja2
|
||
|
|
self.references = {}
|
||
|
|
self._process_templates(references.get("templates", {}))
|
||
|
|
|
||
|
|
@lru_cache(1000)
|
||
|
|
def _render_jinja(u):
|
||
|
|
return jinja2.Template(u).render(**self.templates)
|
||
|
|
|
||
|
|
for k, v in references.get("refs", {}).items():
|
||
|
|
if isinstance(v, str):
|
||
|
|
if v.startswith("base64:"):
|
||
|
|
self.references[k] = base64.b64decode(v[7:])
|
||
|
|
self.references[k] = v
|
||
|
|
elif isinstance(v, dict):
|
||
|
|
self.references[k] = json.dumps(v)
|
||
|
|
elif self.templates:
|
||
|
|
u = v[0]
|
||
|
|
if "{{" in u:
|
||
|
|
if self.simple_templates:
|
||
|
|
u = (
|
||
|
|
u.replace("{{", "{")
|
||
|
|
.replace("}}", "}")
|
||
|
|
.format(**self.templates)
|
||
|
|
)
|
||
|
|
else:
|
||
|
|
u = _render_jinja(u)
|
||
|
|
self.references[k] = [u] if len(v) == 1 else [u, v[1], v[2]]
|
||
|
|
else:
|
||
|
|
self.references[k] = v
|
||
|
|
self.references.update(self._process_gen(references.get("gen", [])))
|
||
|
|
|
||
|
|
def _process_templates(self, tmp):
|
||
|
|
self.templates = {}
|
||
|
|
if self.template_overrides is not None:
|
||
|
|
tmp.update(self.template_overrides)
|
||
|
|
for k, v in tmp.items():
|
||
|
|
if "{{" in v:
|
||
|
|
import jinja2
|
||
|
|
|
||
|
|
self.templates[k] = lambda temp=v, **kwargs: jinja2.Template(
|
||
|
|
temp
|
||
|
|
).render(**kwargs)
|
||
|
|
else:
|
||
|
|
self.templates[k] = v
|
||
|
|
|
||
|
|
def _process_gen(self, gens):
|
||
|
|
out = {}
|
||
|
|
for gen in gens:
|
||
|
|
dimension = {
|
||
|
|
k: v
|
||
|
|
if isinstance(v, list)
|
||
|
|
else range(v.get("start", 0), v["stop"], v.get("step", 1))
|
||
|
|
for k, v in gen["dimensions"].items()
|
||
|
|
}
|
||
|
|
products = (
|
||
|
|
dict(zip(dimension.keys(), values))
|
||
|
|
for values in itertools.product(*dimension.values())
|
||
|
|
)
|
||
|
|
for pr in products:
|
||
|
|
import jinja2
|
||
|
|
|
||
|
|
key = jinja2.Template(gen["key"]).render(**pr, **self.templates)
|
||
|
|
url = jinja2.Template(gen["url"]).render(**pr, **self.templates)
|
||
|
|
if ("offset" in gen) and ("length" in gen):
|
||
|
|
offset = int(
|
||
|
|
jinja2.Template(gen["offset"]).render(**pr, **self.templates)
|
||
|
|
)
|
||
|
|
length = int(
|
||
|
|
jinja2.Template(gen["length"]).render(**pr, **self.templates)
|
||
|
|
)
|
||
|
|
out[key] = [url, offset, length]
|
||
|
|
elif ("offset" in gen) ^ ("length" in gen):
|
||
|
|
raise ValueError(
|
||
|
|
"Both 'offset' and 'length' are required for a "
|
||
|
|
"reference generator entry if either is provided."
|
||
|
|
)
|
||
|
|
else:
|
||
|
|
out[key] = [url]
|
||
|
|
return out
|
||
|
|
|
||
|
|
def _dircache_from_items(self):
|
||
|
|
self.dircache = {"": []}
|
||
|
|
it = self.references.items()
|
||
|
|
for path, part in it:
|
||
|
|
if isinstance(part, (bytes, str)):
|
||
|
|
size = len(part)
|
||
|
|
elif len(part) == 1:
|
||
|
|
size = None
|
||
|
|
else:
|
||
|
|
_, _, size = part
|
||
|
|
par = path.rsplit("/", 1)[0] if "/" in path else ""
|
||
|
|
par0 = par
|
||
|
|
subdirs = [par0]
|
||
|
|
while par0 and par0 not in self.dircache:
|
||
|
|
# collect parent directories
|
||
|
|
par0 = self._parent(par0)
|
||
|
|
subdirs.append(par0)
|
||
|
|
|
||
|
|
subdirs.reverse()
|
||
|
|
for parent, child in zip(subdirs, subdirs[1:]):
|
||
|
|
# register newly discovered directories
|
||
|
|
assert child not in self.dircache
|
||
|
|
assert parent in self.dircache
|
||
|
|
self.dircache[parent].append(
|
||
|
|
{"name": child, "type": "directory", "size": 0}
|
||
|
|
)
|
||
|
|
self.dircache[child] = []
|
||
|
|
|
||
|
|
self.dircache[par].append({"name": path, "type": "file", "size": size})
|
||
|
|
|
||
|
|
def _open(self, path, mode="rb", block_size=None, cache_options=None, **kwargs):
|
||
|
|
data = self.cat_file(path) # load whole chunk into memory
|
||
|
|
return io.BytesIO(data)
|
||
|
|
|
||
|
|
def ls(self, path, detail=True, **kwargs):
|
||
|
|
path = self._strip_protocol(path)
|
||
|
|
if isinstance(self.references, LazyReferenceMapper):
|
||
|
|
try:
|
||
|
|
return self.references.ls(path, detail)
|
||
|
|
except KeyError:
|
||
|
|
pass
|
||
|
|
raise FileNotFoundError(f"'{path}' is not a known key")
|
||
|
|
if not self.dircache:
|
||
|
|
self._dircache_from_items()
|
||
|
|
out = self._ls_from_cache(path)
|
||
|
|
if out is None:
|
||
|
|
raise FileNotFoundError(path)
|
||
|
|
if detail:
|
||
|
|
return out
|
||
|
|
return [o["name"] for o in out]
|
||
|
|
|
||
|
|
def exists(self, path, **kwargs): # overwrite auto-sync version
|
||
|
|
return self.isdir(path) or self.isfile(path)
|
||
|
|
|
||
|
|
def isdir(self, path): # overwrite auto-sync version
|
||
|
|
if self.dircache:
|
||
|
|
return path in self.dircache
|
||
|
|
elif isinstance(self.references, LazyReferenceMapper):
|
||
|
|
return path in self.references.listdir("")
|
||
|
|
else:
|
||
|
|
# this may be faster than building dircache for single calls, but
|
||
|
|
# by looping will be slow for many calls; could cache it?
|
||
|
|
return any(_.startswith(f"{path}/") for _ in self.references)
|
||
|
|
|
||
|
|
def isfile(self, path): # overwrite auto-sync version
|
||
|
|
return path in self.references
|
||
|
|
|
||
|
|
async def _ls(self, path, detail=True, **kwargs): # calls fast sync code
|
||
|
|
return self.ls(path, detail, **kwargs)
|
||
|
|
|
||
|
|
def find(self, path, maxdepth=None, withdirs=False, detail=False, **kwargs):
|
||
|
|
if withdirs:
|
||
|
|
return super().find(
|
||
|
|
path, maxdepth=maxdepth, withdirs=withdirs, detail=detail, **kwargs
|
||
|
|
)
|
||
|
|
if path:
|
||
|
|
path = self._strip_protocol(path)
|
||
|
|
r = sorted(k for k in self.references if k.startswith(path))
|
||
|
|
else:
|
||
|
|
r = sorted(self.references)
|
||
|
|
if detail:
|
||
|
|
if not self.dircache:
|
||
|
|
self._dircache_from_items()
|
||
|
|
return {k: self._ls_from_cache(k)[0] for k in r}
|
||
|
|
else:
|
||
|
|
return r
|
||
|
|
|
||
|
|
def info(self, path, **kwargs):
|
||
|
|
out = self.references.get(path)
|
||
|
|
if out is not None:
|
||
|
|
if isinstance(out, (str, bytes)):
|
||
|
|
# decode base64 here
|
||
|
|
return {"name": path, "type": "file", "size": len(out)}
|
||
|
|
elif len(out) > 1:
|
||
|
|
return {"name": path, "type": "file", "size": out[2]}
|
||
|
|
else:
|
||
|
|
out0 = [{"name": path, "type": "file", "size": None}]
|
||
|
|
else:
|
||
|
|
out = self.ls(path, True)
|
||
|
|
out0 = [o for o in out if o["name"] == path]
|
||
|
|
if not out0:
|
||
|
|
return {"name": path, "type": "directory", "size": 0}
|
||
|
|
if out0[0]["size"] is None:
|
||
|
|
# if this is a whole remote file, update size using remote FS
|
||
|
|
prot, _ = split_protocol(self.references[path][0])
|
||
|
|
out0[0]["size"] = self.fss[prot].size(self.references[path][0])
|
||
|
|
return out0[0]
|
||
|
|
|
||
|
|
async def _info(self, path, **kwargs): # calls fast sync code
|
||
|
|
return self.info(path)
|
||
|
|
|
||
|
|
async def _rm_file(self, path, **kwargs):
|
||
|
|
self.references.pop(
|
||
|
|
path, None
|
||
|
|
) # ignores FileNotFound, just as well for directories
|
||
|
|
self.dircache.clear() # this is a bit heavy handed
|
||
|
|
|
||
|
|
async def _pipe_file(self, path, data):
|
||
|
|
# can be str or bytes
|
||
|
|
self.references[path] = data
|
||
|
|
self.dircache.clear() # this is a bit heavy handed
|
||
|
|
|
||
|
|
async def _put_file(self, lpath, rpath, **kwargs):
|
||
|
|
# puts binary
|
||
|
|
with open(lpath, "rb") as f:
|
||
|
|
self.references[rpath] = f.read()
|
||
|
|
self.dircache.clear() # this is a bit heavy handed
|
||
|
|
|
||
|
|
def save_json(self, url, **storage_options):
|
||
|
|
"""Write modified references into new location"""
|
||
|
|
out = {}
|
||
|
|
for k, v in self.references.items():
|
||
|
|
if isinstance(v, bytes):
|
||
|
|
try:
|
||
|
|
out[k] = v.decode("ascii")
|
||
|
|
except UnicodeDecodeError:
|
||
|
|
out[k] = (b"base64:" + base64.b64encode(v)).decode()
|
||
|
|
else:
|
||
|
|
out[k] = v
|
||
|
|
with fsspec.open(url, "wb", **storage_options) as f:
|
||
|
|
f.write(json.dumps({"version": 1, "refs": out}).encode())
|