Source code for fsspec.implementations.reference

import base64
import io
import itertools
import logging
from functools import lru_cache

try:
    import ujson as json
except ImportError:
    import json

from ..asyn import AsyncFileSystem, sync
from ..callbacks import _DEFAULT_CALLBACK
from ..core import filesystem, open
from ..mapping import get_mapper
from ..spec import AbstractFileSystem

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


[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)} https://github.com/intake/fsspec-reference-maker/blob/main/README.md """ 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=False, loop=None, ref_type=None, **kwargs, ): """ Parameters ---------- fo : dict or str The set of references to use for this instance, with a structure as above. If str, will use fsspec.open, in conjunction with ref_storage_args to open and parse JSON at this location. 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 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, if given as a path remote_protocol : str The protocol of the filesystem on which the references will be evaluated (unless fs is provided) remote_options : dict kwargs to go with remote_protocol fs : file system instance Directly provide a file system, if you want to configure it beforehand. This takes precedence over target_protocol/target_options template_overrides : dict Swap out any templates in the references file with these - useful for testing. ref_type : "json" | "parquet" | "zarr" If None, guessed from URL suffix, defaulting to JSON. Ignored if fo is not a string. simple_templates: bool kwargs : passed to parent class """ super().__init__(loop=loop, **kwargs) self.target = target self.dataframe = False self.template_overrides = template_overrides self.simple_templates = simple_templates if hasattr(fo, "read"): text = fo.read() elif isinstance(fo, str): if target_protocol: extra = {"protocol": target_protocol} else: extra = {} dic = dict(**(ref_storage_args or target_options or {}), **extra) if ref_type == "zarr" or fo.endswith("zarr"): import pandas as pd import zarr self.dataframe = True m = get_mapper(fo, **dic) z = zarr.open_group(m) assert z.attrs["version"] == 1 self.templates = z.attrs["templates"] self.gen = z.attrs.get("gen", None) self.df = pd.DataFrame( {k: z[k][:] for k in ["key", "data", "url", "offset", "size"]} ).set_index("key") elif ref_type == "parquet" or fo.endswith("parquet"): import fastparquet as fp self.dataframe = True with open(fo, "rb", **dic) as f: pf = fp.ParquetFile(f) assert pf.key_value_metadata["version"] == 1 self.templates = json.loads(pf.key_value_metadata["templates"]) self.gen = json.loads(pf.key_value_metadata.get("gen", "[]")) self.df = pf.to_pandas(index="key") else: # text JSON with open(fo, "rb", **dic) as f: logger.info("Read reference from URL %s", fo) text = f.read() else: # dictionaries; TODO: allow dataframe here? text = fo if self.dataframe: self._process_dataframe() else: self._process_references(text, template_overrides) if fs is None and remote_protocol is None: remote_protocol = target_protocol if remote_protocol: fs = filesystem(remote_protocol, loop=loop, **(remote_options or {})) self.fs = fs
@property def loop(self): return self.fs.loop if self.fs.async_impl else self._loop def _cat_common(self, path): path = self._strip_protocol(path) logger.debug(f"cat: {path}") # TODO: can extract and cache templating here if self.dataframe: part = self.df.loc[path] if part["data"]: part = part["data"] else: part = part[["url", "offset", "size"]] else: part = self.references[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") url = part[0] start = None end = None else: url, start, size = part logger.debug(f"Reference: {path}, offset {start}, size {size}") end = start + size if url is None: url = self.target return url, start, end async def _cat_file(self, path, start=None, end=None, **kwargs): part_or_url, start0, end0 = self._cat_common(path) if isinstance(part_or_url, bytes): return part_or_url[start:end] return (await self.fs._cat_file(part_or_url, start=start0, end=end0))[start:end] def cat_file(self, path, start=None, end=None, **kwargs): part_or_url, start0, end0 = self._cat_common(path) if isinstance(part_or_url, bytes): return part_or_url[start:end] return self.fs.cat_file(part_or_url, start=start0, end=end0)[start:end] 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): 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): data = self.cat_file(rpath, **kwargs) callback.lazy_call("set_size", len, data) with open(lpath, "wb") as f: f.write(data) callback.lazy_call("absolute_update", len, data) def get(self, rpath, lpath, recursive=False, **kwargs): if self.fs.async_impl: return sync(self.loop, self._get, rpath, lpath, recursive, **kwargs) return AbstractFileSystem.get(rpath, lpath, recursive=recursive, **kwargs) def cat(self, path, recursive=False, **kwargs): if self.fs.async_impl: return sync(self.loop, self._cat, path, recursive, **kwargs) elif isinstance(path, list): if recursive or any("*" in p for p in path): raise NotImplementedError return {p: AbstractFileSystem.cat_file(self, p, **kwargs) for p in path} else: return AbstractFileSystem.cat_file(self, path) def _process_dataframe(self): self._process_templates(self.templates) @lru_cache(1000) def _render_jinja(url): import jinja2 if "{{" in url: if self.simple_templates: return ( url.replace("{{", "{") .replace("}}", "}") .format(**self.templates) ) return jinja2.Template(url).render(**self.templates) return url if self.templates: self.df["url"] = self.df["url"].map(_render_jinja) self._dircache_from_items() def _process_references(self, references, template_overrides=None): if isinstance(references, (str, bytes)): references = json.loads(references) 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? self._dircache_from_items() def _process_references0(self, references): """Make reference dict for Spec Version 0""" if "zarr_consolidated_format" in references: # special case for Ike prototype references = _unmodel_hdf5(references) self.references = references def _process_references1(self, references, template_overrides=None): try: import jinja2 except ImportError as e: raise ValueError("Reference Spec Version 1 requires jinja2") from e 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 else: 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]] self.references.update(self._process_gen(references.get("gen", []))) def _process_templates(self, tmp): import jinja2 self.templates = {} if self.template_overrides is not None: tmp.update(self.template_overrides) for k, v in tmp.items(): if "{{" in v: self.templates[k] = lambda temp=v, **kwargs: jinja2.Template( temp ).render(**kwargs) else: self.templates[k] = v def _process_gen(self, gens): import jinja2 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: 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 = {"": []} if self.dataframe: it = self.df.iterrows() else: it = self.references.items() for path, part in it: if self.dataframe: if part["data"]: size = len(part["data"]) else: size = part["size"] else: if isinstance(part, (bytes, str)): size = len(part) elif len(part) == 1: size = None else: _, start, size = part par = self._parent(path) par0 = par while par0 and par0 not in self.dircache: # build parent directories self.dircache[par0] = [] self.dircache.setdefault(self._parent(par0), []).append( {"name": par0, "type": "directory", "size": 0} ) par0 = self._parent(par0) self.dircache[par].append({"name": path, "type": "file", "size": size}) def open(self, path, mode="rb", block_size=None, cache_options=None, **kwargs): if mode != "rb": raise NotImplementedError 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) out = self._ls_from_cache(path) if out is None: raise FileNotFoundError if detail: return out return [o["name"] for o in out] def exists(self, path, **kwargs): # overwrite auto-sync version try: return self._ls_from_cache(path) is not None except FileNotFoundError: return False def isdir(self, path): # overwrite auto-sync version return self.exists(path) and self.info(path)["type"] == "directory" def isfile(self, path): # overwrite auto-sync version return self.exists(path) and self.info(path)["type"] == "file" async def _ls(self, path, detail=True, **kwargs): # calls fast sync code return self.ls(path, detail, **kwargs) def info(self, path, **kwargs): 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} return out0[0] async def _info(self, path, **kwargs): # calls fast sync code return self.info(path)
def _unmodel_hdf5(references): """Special JSON format from HDF5 prototype""" # see https://gist.github.com/ajelenak/80354a95b449cedea5cca508004f97a9 import re ref = {} for key, value in references["metadata"].items(): if key.endswith(".zchunkstore"): source = value.pop("source")["uri"] match = re.findall(r"https://([^.]+)\.s3\.amazonaws\.com", source) if match: source = source.replace( f"https://{match[0]}.s3.amazonaws.com", match[0] ) for k, v in value.items(): ref[k] = (source, v["offset"], v["offset"] + v["size"]) else: ref[key] = json.dumps(value).encode() return ref