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Add parquet reference docs
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martindurant committed Feb 8, 2024
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Expand Up @@ -138,3 +138,69 @@ from the given URL, at an offset of 1000.

<script data-goatcounter="https://kerchunk.goatcounter.com/count"
async src="//gc.zgo.at/count.js"></script>

Parquet references
------------------

Since JSON is rather verbose, it is easy with enough chunks to make a references file
that is too big: slow to load and heavy on memory. Although the former can be
alleviated by compression (I recommend Zstd), the latter cannot. This can
become particularly apparent during the combine phase when loading many reference sets.

The class `fsspec.implementations.reference.LazyReferenceMapper`_ provides an
alternative _implementation_, and its on-disk layout effectively is a new reference
spec, and we describe it here. The class itself has a dict mapper interface, just
like the rendered references from JSON files; except that it assumes that it is
working on a zarr dataset. This is because the references are split into files, and
an array's shape/chunk information is used to figure out which reference file
to load.

.. _fsspec.implementations.reference.LazyReferenceMapper: https://filesystem-spec.readthedocs.io/en/latest/api.html?highlight=lazyreference#fsspec.implementations.reference.LazyReferenceMapper

The following code

.. code-block:: python
lz = fsspec.implementations.reference.LazyReferenceMapper.create("ref.parquet")
z = zarr.open_group(lz, mode="w")
d = z.create_dataset("name", shape=(1,))
d[:] = 1
g2 = z.create_group("deep")
d = g2.create_dataset("name", shape=(1,))
d[:] = 1
produces files

.. code-block:: text
ref.parquet/deep/name/refs.0.parq
ref.parquet/name/refs.0.parq
ref.parquet/.zmetadata
Here, .zmetadata is all of the metadata of all of all subgroups/arrays (similar to
zarr "consolidated metadata", with two top-level fields: "metadata" (dict[str, str] all of the
zarr metadata key/values) and "record_size", an integer set during ``.create()``.

Each parquet file contains references within the corresponding path to where it is.
For example, key "name/0" will be the zeroth reference in "./name/refs.0.parq". If
there are multiple dimensions, normal C indexing is used to find the Nth reference,
and there are up to "record_size" references (default 10000) in the first file;
reference >10000,<=2000 would be in "./name/refs.2.parquet". Each file is (for now)
padded to record_size, but they compress really well.

Each row of the parquet data contains fields

.. code-block::
path: optional str/categorical, remote location URL
offset: int, start location of block
size: int, number of bytes in block
raw: optional bytes, binary data
If ``raw`` is populated, this is the data of the key. If ``path`` is
populated but size is 0, it is the whole file indicated. Otherwise,
it is a byte block in the indicated file. If both ``raw`` and ``path``
are NULL, the key does not exist.

We reserve the possibility to store small array data in .zmetadata instead
of creating a small/mostly empty parquet file for each.

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