Source code for fsspec.implementations.reference

import base64
import collections
import io
import itertools
import logging
import math
import os
from functools import lru_cache
from typing import TYPE_CHECKING

import fsspec.core

    import ujson as json
except ImportError:
    if not TYPE_CHECKING:
        import json

from ..asyn import AsyncFileSystem
from ..callbacks import DEFAULT_CALLBACK
from ..core import filesystem, open, split_protocol
from ..utils import isfilelike, merge_offset_ranges, other_paths

logger = logging.getLogger("fsspec.reference")

class ReferenceNotReachable(RuntimeError):
    def __init__(self, reference, target, *args):
        self.reference = reference = target

    def __str__(self):
        return f'Reference "{self.reference}" failed to fetch target {}'

def _first(d):
    return list(d.values())[0]

def _prot_in_references(path, references):
    ref = references.get(path)
    if isinstance(ref, (list, tuple)):
        return split_protocol(ref[0])[0] if ref[0] else ref[0]

def _protocol_groups(paths, references):
    if isinstance(paths, str):
        return {_prot_in_references(paths, references): [paths]}
    out = {}
    for path in paths:
        protocol = _prot_in_references(path, references)
        out.setdefault(protocol, []).append(path)
    return out

class RefsValuesView(
    def __iter__(self):
        for val in self._mapping.zmetadata.values():
            yield json.dumps(val).encode()
        yield from self._mapping._items.values()
        for field in self._mapping.listdir():
            chunk_sizes = self._mapping._get_chunk_sizes(field)
            if len(chunk_sizes) == 0:
                yield self._mapping[field + "/0"]
            yield from self._mapping._generate_all_records(field)

class RefsItemsView(
    def __iter__(self):
        return zip(self._mapping.keys(), self._mapping.values())

def ravel_multi_index(idx, sizes):
    val = 0
    mult = 1
    for i, s in zip(idx[::-1], sizes[::-1]):
        val += i * mult
        mult *= s
    return val

[docs]class LazyReferenceMapper( """This interface can be used to read/write references from Parquet stores. It is not intended for other types of references. It can be used with Kerchunk's MultiZarrToZarr method to combine references into a parquet store. Examples of this use-case can be found here:""" # import is class level to prevent numpy dep requirement for fsspec @property def np(self): import numpy as np return np @property def pd(self): import pandas as pd return pd
[docs] def __init__( self, root, fs=None, out_root=None, cache_size=128, categorical_threshold=10 ): """ This instance will be writable, storing changes in memory until full partitions are accumulated or .flush() is called. To create an empty lazy store, use .create() Parameters ---------- root : str Root of parquet store fs : fsspec.AbstractFileSystem fsspec filesystem object, default is local filesystem. cache_size : int, default=128 Maximum size of LRU cache, where cache_size*record_size denotes the total number of references that can be loaded in memory at once. categorical_threshold : int Encode urls as pandas.Categorical to reduce memory footprint if the ratio of the number of unique urls to total number of refs for each variable is greater than or equal to this number. (default 10) """ self.root = root self.chunk_sizes = {} self.out_root = out_root or self.root self.cat_thresh = categorical_threshold self.cache_size = cache_size self.dirs = None self.url = self.root + "/{field}/refs.{record}.parq" # TODO: derive fs from `root` self.fs = fsspec.filesystem("file") if fs is None else fs
def __getattr__(self, item): if item in ("_items", "record_size", "zmetadata"): self.setup() # avoid possible recursion if setup fails somehow return self.__dict__[item] raise AttributeError(item) def setup(self): self._items = {} self._items[".zmetadata"] = self.fs.cat_file( "/".join([self.root, ".zmetadata"]) ) met = json.loads(self._items[".zmetadata"]) self.record_size = met["record_size"] self.zmetadata = met["metadata"] # Define function to open and decompress refs @lru_cache(maxsize=self.cache_size) def open_refs(field, record): """cached parquet file loader""" path = self.url.format(field=field, record=record) data = io.BytesIO(self.fs.cat_file(path)) df = self.pd.read_parquet(data, engine="fastparquet") refs = {c: df[c].values for c in df.columns} return refs self.open_refs = open_refs @staticmethod def create(root, storage_options=None, fs=None, record_size=10000, **kwargs): """Make empty parquet reference set First deletes the contents of the given directory, if it exists. Parameters ---------- root: str Directory to contain the output; will be created storage_options: dict | None For making the filesystem to use for writing is fs is None fs: FileSystem | None Filesystem for writing record_size: int Number of references per parquet file kwargs: passed to __init__ Returns ------- LazyReferenceMapper instance """ met = {"metadata": {}, "record_size": record_size} if fs is None: fs, root = fsspec.core.url_to_fs(root, **(storage_options or {})) if fs.exists(root): fs.rm(root, recursive=True) fs.makedirs(root, exist_ok=True) fs.pipe("/".join([root, ".zmetadata"]), json.dumps(met).encode()) return LazyReferenceMapper(root, fs, **kwargs) def listdir(self, basename=True): """List top-level directories""" # cache me? if self.dirs is None: dirs = [p.split("/", 1)[0] for p in self.zmetadata] self.dirs = {p for p in dirs if p and not p.startswith(".")} listing = self.dirs if basename: listing = [os.path.basename(path) for path in listing] return listing def ls(self, path="", detail=True): """Shortcut file listings""" if not path: dirnames = self.listdir() others = set( [".zmetadata"] + [name for name in self.zmetadata if "/" not in name] + [name for name in self._items if "/" not in name] ) if detail is False: others.update(dirnames) return sorted(others) dirinfo = [ {"name": name, "type": "directory", "size": 0} for name in dirnames ] fileinfo = [ { "name": name, "type": "file", "size": len( json.dumps(self.zmetadata[name]) if name in self.zmetadata else self._items[name] ), } for name in others ] return sorted(dirinfo + fileinfo, key=lambda s: s["name"]) parts = path.split("/", 1) if len(parts) > 1: raise FileNotFoundError("Cannot list within directories right now") field = parts[0] others = set( [name for name in self.zmetadata if name.startswith(f"{path}/")] + [name for name in self._items if name.startswith(f"{path}/")] ) fileinfo = [ { "name": name, "type": "file", "size": len( json.dumps(self.zmetadata[name]) if name in self.zmetadata else self._items[name] ), } for name in others ] keys = self._keys_in_field(field) if detail is False: return list(others) + list(keys) recs = self._generate_all_records(field) recinfo = [ {"name": name, "type": "file", "size": rec[-1]} for name, rec in zip(keys, recs) if rec[0] # filters out path==None, deleted/missing ] return fileinfo + recinfo def _load_one_key(self, key): """Get the reference for one key Returns bytes, one-element list or three-element list. """ if key in self._items: return self._items[key] elif key in self.zmetadata: return json.dumps(self.zmetadata[key]).encode() elif "/" not in key or self._is_meta(key): raise KeyError(key) field, sub_key = key.split("/") record, ri, chunk_size = self._key_to_record(key) maybe = self._items.get((field, record), {}).get(ri, False) if maybe is None: # explicitly deleted raise KeyError elif maybe: return maybe elif chunk_size == 0: return b"" # Chunk keys can be loaded from row group and cached in LRU cache try: refs = self.open_refs(field, record) except (ValueError, TypeError, FileNotFoundError): raise KeyError(key) columns = ["path", "offset", "size", "raw"] selection = [refs[c][ri] if c in refs else None for c in columns] raw = selection[-1] if raw is not None: return raw if selection[0] is None: raise KeyError("This reference does not exist or has been deleted") if selection[1:3] == [0, 0]: # URL only return selection[:1] # URL, offset, size return selection[:3] @lru_cache(4096) def _key_to_record(self, key): """Details needed to construct a reference for one key""" field, chunk = key.split("/") chunk_sizes = self._get_chunk_sizes(field) if len(chunk_sizes) == 0: return 0, 0, 0 chunk_idx = [int(c) for c in chunk.split(".")] chunk_number = ravel_multi_index(chunk_idx, chunk_sizes) record = chunk_number // self.record_size ri = chunk_number % self.record_size return record, ri, len(chunk_sizes) def _get_chunk_sizes(self, field): """The number of chunks along each axis for a given field""" if field not in self.chunk_sizes: zarray = self.zmetadata[f"{field}/.zarray"] size_ratio = [ math.ceil(s / c) for s, c in zip(zarray["shape"], zarray["chunks"]) ] self.chunk_sizes[field] = size_ratio or [1] 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) it = iter(zip(*refs.values())) if len(refs) == 3: # All urls return (list(t) for t in it) elif len(refs) == 1: # All raws return refs["raw"] else: # Mix of urls and raws 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): nrec *= ch 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.split("/") 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, chunk = key.split("/") 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 += 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])
[docs]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)} """ protocol = "reference"
[docs] 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, 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) = 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, "rb", **dic) as f:"Read reference from URL %s", fo) text = json.load(f) self._process_references(text, template_overrides) else: # Lazy parquet refs"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 = 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"") rpath = self.expand_path(rpath, recursive=recursive) fs = fsspec.filesystem("file", auto_mkdir=True) targets = other_paths(rpath, lpath) if recursive: data =[r for r in rpath if not self.isdir(r)]) else: data = 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""" 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 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 = subdirs[::-1] 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, 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, 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 =, 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 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] = 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, "wb", **storage_options) as f: f.write(json.dumps({"version": 1, "refs": out}).encode())