import base64
import io
import itertools
import logging
import os
from functools import lru_cache
import fsspec.core
try:
import ujson as json
except ImportError:
import json
from ..asyn import AsyncFileSystem, sync
from ..callbacks import _DEFAULT_CALLBACK
from ..core import filesystem, open, split_protocol
from ..spec import AbstractFileSystem
logger = logging.getLogger("fsspec.reference")
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
[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/fsspec/kerchunk/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=True,
loop=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). 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.
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
self.templates = {}
self.fss = {}
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)
# text JSON
with open(fo, "rb", **dic) as f:
logger.info("Read reference from URL %s", fo)
text = f.read()
else:
# dictionaries
text = fo
if self.dataframe:
self._process_dataframe()
else:
self._process_references(text, 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()
}
return
if fs is not None:
# single remote FS
remote_protocol = (
fs.protocol[0] if isinstance(fs.protocol, tuple) else fs.protocol
)
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:
remote_protocol = protocol
break
if remote_protocol is None:
# get single protocol from references
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:
remote_protocol = protocol
break
if remote_protocol is None:
remote_protocol = target_protocol
fs = fs or filesystem(remote_protocol, loop=loop, **(remote_options or {}))
self.fss[remote_protocol] = fs
self.fss[None] = fs # default one
@property
def loop(self):
inloop = [fs.loop for fs in self.fss.values() if fs.async_impl]
return inloop[0] if inloop 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]
protocol, _ = split_protocol(part_or_url)
# TODO: start and end should be passed to cat_file, not sliced
return (
await self.fss[protocol]._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]
protocol, _ = split_protocol(part_or_url)
# TODO: start and end should be passed to cat_file, not sliced
return self.fss[protocol].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):
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))
with open(lpath, "wb") as f:
f.write(data)
callback.absolute_update(len(data))
def get(self, rpath, lpath, recursive=False, **kwargs):
if isinstance(lpath, list):
# because we have to figure out here which lpath goes with which path
# after grouping
raise NotImplementedError
proto_dict = _protocol_groups(rpath, self.references)
for proto, paths in proto_dict.items():
if self.fss[proto].async_impl:
sync(self.loop, self._get, paths, lpath, recursive, **kwargs)
else:
AbstractFileSystem.get(
self, paths, lpath, recursive=recursive, **kwargs
)
def cat(self, path, recursive=False, on_error="raise", **kwargs):
proto_dict = _protocol_groups(path, self.references)
out = {}
for proto, paths in proto_dict.items():
if proto is None:
# binary/string
for p in paths:
try:
out[p] = AbstractFileSystem.cat_file(self, p, **kwargs)
except Exception as e:
if on_error == "raise":
raise
if on_error == "return":
out[p] = e
elif self.fss[proto].async_impl:
# TODO: asyncio.gather on multiple async FSs
out.update(
sync(
self.loop,
self._cat,
paths,
recursive,
on_error=on_error,
**kwargs,
)
)
elif isinstance(paths, list):
if recursive or any("*" in p for p in paths):
raise NotImplementedError
for p in paths:
try:
out[p] = AbstractFileSystem.cat_file(self, p, **kwargs)
except Exception as e:
if on_error == "raise":
raise
if on_error == "return":
out[p] = e
else:
out.update(AbstractFileSystem.cat_file(self, paths))
if len(out) == 1 and isinstance(path, str) and "*" not in path:
return _first(out)
return out
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)
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?
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):
if not self.simple_templates or self.templates:
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
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):
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 = path.rsplit("/", 1)[0] if "/" in path else ""
par0 = par
while par0 and par0 not in self.dircache:
# build parent directories
self.dircache[par0] = []
self.dircache.setdefault(
par0.rsplit("/", 1)[0] if "/" in par0 else "", []
).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)
if not self.dircache:
self._dircache_from_items()
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
return self.isdir(path) or self.isfile(path)
def isdir(self, path): # overwrite auto-sync version
if self.dircache:
return path in self.dircache
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, **kwargs):
if withdirs:
return super().find(path, maxdepth=maxdepth, withdirs=withdirs, **kwargs)
if path:
path = self._strip_protocol(path)
return sorted(k for k in self.references if k.startswith(path))
return sorted(self.references)
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}
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)
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