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import io
import fsspec
import json
import kerchunk.utils
import kerchunk.zarr
import numpy as np
import pytest
import zarr
from fsspec.implementations.asyn_wrapper import AsyncFileSystemWrapper
def test_rename():
old = {"version": 1, "refs": {"v0": ["oldpath", 0, 0], "bin": "data"}}
new = kerchunk.utils.rename_target(old, {"oldpath": "newpath"})
assert new == {"version": 1, "refs": {"v0": ["newpath", 0, 0], "bin": "data"}}
def test_rename_files(m):
m.pipe(
"ref.json", b'{"version": 1, "refs": {"v0": ["oldpath", 0, 0], "bin": "data"}}'
)
kerchunk.utils.rename_target_files("memory://ref.json", {"oldpath": "newpath"})
out = m.cat("ref.json")
assert out == b'{"version":1,"refs":{"v0":["newpath",0,0],"bin":"data"}}'
kerchunk.utils.rename_target_files(
"memory://ref.json", {"newpath": "newerpath"}, url_out="memory://ref2.json"
)
out = m.cat("ref.json")
assert out == b'{"version":1,"refs":{"v0":["newpath",0,0],"bin":"data"}}'
out = m.cat("ref2.json")
assert out == b'{"version":1,"refs":{"v0":["newerpath",0,0],"bin":"data"}}'
def test_inline(m):
m.pipe("data", b"stuff")
refs = {
"key0": b"00",
"key1": ["memory://data"],
"key2": ["memory://data", 1, 1],
"key1": ["memory://data", 2, 4],
}
out = kerchunk.utils.do_inline(refs, 2)
expected = {
"key0": b"00",
"key1": ["memory://data"],
"key2": b"t",
"key1": ["memory://data", 2, 4],
}
assert out == expected
def test_inline_array():
refs = {
".zgroup": b'{"zarr_format": 2}',
"data/.zarray": """
{
"chunks": [
1
],
"compressor": null,
"dtype": "<i4",
"fill_value": 0,
"filters": null,
"order": "C",
"shape": [
2
],
"zarr_format": 2
}
""",
"data/0": b"\x01\x00\x00\x00",
"data/1": b"\x02\x00\x00\x00",
"data/.zattrs": '{"foo": "bar"}',
}
out1 = kerchunk.utils.inline_array(refs, threshold=1) # does nothing
assert out1 == refs
out2 = kerchunk.utils.inline_array(refs, threshold=1, names=["data"]) # explicit
assert json.loads(out2["data/.zattrs"]) == json.loads(refs["data/.zattrs"])
localfs = fsspec.filesystem("file")
store = kerchunk.utils.refs_as_store(out2, fs=localfs)
g = zarr.open(store, mode="r", zarr_format=2)
assert g["data"][:].tolist() == [1, 2] # What is g.data???
out3 = kerchunk.utils.inline_array(refs, threshold=1000) # inlines because of size
store = kerchunk.utils.refs_as_store(out3, localfs)
g = zarr.open(store, mode="r", zarr_format=2)
assert g["data"][:].tolist() == [1, 2] # What is g.data???
def test_json():
data = {"a": "a", "b": b"b", "c": [None, None, None], "d": '{"key": 0}'}
out = kerchunk.utils._encode_for_JSON(data)
expected = {"a": "a", "b": "b", "c": [None, None, None], "d": '{"key":0}'}
assert out == expected
@pytest.mark.parametrize("chunks", [[10, 10], [5, 10]])
def test_subchunk_exact(m, chunks):
g = zarr.open_group("memory://test.zarr", mode="w", zarr_format=2)
data = np.arange(100).reshape(10, 10)
arr = g.create_array(
"data", dtype=data.dtype, shape=data.shape, chunks=chunks, compressor=None
)
arr[:] = data
ref = kerchunk.zarr.single_zarr("memory://test.zarr")["refs"]
extra = [] if chunks[0] == 10 else ["data/1.0"]
ref2 = list(_ for _ in ref if not _.endswith("zattrs")) # ignore empty attrs
assert ref2 == [".zgroup", "data/.zarray", "data/0.0"] + extra
out = kerchunk.utils.subchunk(ref, "data", 5)
nchunk = 10 // chunks[0] * 5
out2 = list(_ for _ in out if not _.endswith("zattrs"))
assert out2 == [".zgroup", "data/.zarray"] + [f"data/{_}.0" for _ in range(nchunk)]
store = kerchunk.utils.refs_as_store(out, remote_protocol="memory")
g2 = zarr.open_group(store, mode="r", zarr_format=2)
# g2 = zarr.open_group(
# "reference://", storage_options={"fo": out, "remote_protocol": "memory"}, zarr_format=2
# )
assert (g2["data"][:] == data).all()
@pytest.mark.parametrize("archive", ["zip", "tar"])
def test_archive(m, archive):
import zipfile
import tarfile
data = b"piece of data"
with fsspec.open("memory://archive", "wb") as f:
if archive == "zip":
arc = zipfile.ZipFile(file=f, mode="w")
arc.writestr("data1", data)
arc.close()
else:
arc = tarfile.TarFile(fileobj=f, mode="w")
ti = tarfile.TarInfo("data1")
ti.size = len(data)
arc.addfile(ti, io.BytesIO(data))
arc.close()
refs = {
"a": b"stuff",
"b": [f"{archive}://data1::memory://archive"],
"c": [f"{archive}://data1::memory://archive", 5, 2],
}
refs2 = kerchunk.utils.dereference_archives(refs)
fs = fsspec.filesystem("reference", fo=refs2)
assert fs.cat("a") == b"stuff"
assert fs.cat("b") == data
assert fs.cat("c") == data[5:7]
def test_deflate_zip_archive(m):
import zipfile
from kerchunk.codecs import DeflateCodec
dec = DeflateCodec()
data = b"piece of data"
with fsspec.open("memory://archive", "wb") as f:
arc = zipfile.ZipFile(file=f, mode="w", compression=zipfile.ZIP_DEFLATED)
arc.writestr("data1", data)
arc.close()
refs = {
"b": [f"zip://data1::memory://archive"],
}
with pytest.warns(UserWarning):
refs2 = kerchunk.utils.dereference_archives(refs)
fs = fsspec.filesystem("reference", fo=refs2)
assert dec.decode(fs.cat("b")) == data
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