Coalesce parquet files

coalesce_parquet.py

"""coalesce_parquets.py

gist of how to coalesce small row groups into larger row groups.
Solves the problem described in https://issues.apache.org/jira/browse/PARQUET-1115
"""
from __future__ import annotations

from pathlib import Path
from typing import Callable, Iterable, TypeVar

import pyarrow as pa
import pyarrow.parquet as pq


def stream_to_parquet(path: Path, tables: Iterable[pa.Table]) -> None:
    try:
        first = next(tables)
    except StopIteration:
        return
    schema = first.schema
    with pq.ParquetWriter(path, schema) as writer:
        writer.write_table(first)
        for table in tables:
            table = table.cast(schema)  # enforce schema
            writer.write_table(table)


def stream_from_parquet(path: Path) -> Iterable[pa.Table]:
    reader = pq.ParquetFile(path)
    for batch in reader.iter_batches():
        yield pa.Table.from_batches([batch])


def stream_from_parquets(paths: Iterable[Path]) -> Iterable[pa.Table]:
    for path in paths:
        yield from stream_from_parquet(path)


T = TypeVar("T")


def coalesce(
    items: Iterable[T], max_size: int, sizer: Callable[[T], int] = len
) -> Iterable[list[T]]:
    """Coalesce items into chunks. Tries to maximize chunk size and not exceed max_size.

    If an item is larger than max_size, we will always exceed max_size, so make a
    best effort and place it in its own chunk.

    You can supply a custom sizer function to determine the size of an item.
    Default is len.

    >>> list(coalesce([1, 2, 11, 4, 4, 1, 2], 10, lambda x: x))
    [[1, 2], [11], [4, 4, 1], [2]]
    """
    batch = []
    current_size = 0
    for item in items:
        this_size = sizer(item)
        if current_size + this_size > max_size:
            yield batch
            batch = []
            current_size = 0
        batch.append(item)
        current_size += this_size
    if batch:
        yield batch


def coalesce_parquets(paths: Iterable[Path], outpath: Path, max_size: int = 2**20) -> None:
    tables = stream_from_parquets(paths)
    # Instead of coalescing using number of rows as your metric, you could
    # use pa.Table.nbytes or something.
    # table_groups = coalesce(tables, max_size, sizer=lambda t: t.nbytes)
    table_groups = coalesce(tables, max_size)
    coalesced_tables = (pa.concat_tables(group) for group in table_groups)
    stream_to_parquet(outpath, coalesced_tables)
    

paths = Path("in_dir").glob("*.parquet")
coalesce_parquets(paths, "out.parquet")

It works fine for me with a few test parquet files. I'm on 3.10, but I wouldn't think 3.7 would be a problem. I'd imagine it's something external to the script, such as

• Are those paths correct? Test by opening one of the files in the input dir using eg pandas or pyarrow
• Do the input parquets actually have >0 rows?
• Some sort of permissions errors? Can you write that output parquet using pandas.DataFrame.to_parquet()?

Insert some debug print statements in there and see where something unexpected is happening.

this is awesome, thank you

What about performance and memory usage?

At first look - The method coalesce loads all data from parquet files into memory.
Also it make sense to filter files that do not make sense to coalesce.

What about performance and memory usage?

At first look - The method coalesce loads all data from parquet files into memory.

coalesce() doesn't load ALL data into memory, it loads them until the batch size is over the threshold, then yields that batch and then deletes that batch. So it will hold up to ~max_size amount of data in memory at a time. At least that was the intention, perhaps there is a bug in there where I'm not actually freeing the memory. If you have profiled or have some evidence of this, please let me know.

Also it make sense to filter files that do not make sense to coalesce.

Not sure what you mean here?

This is great!

Adding a small reproducible example of how this works below (the following code creates some directories)

import os
import pandas as pd
import pyarrow.parquet as pq

home = os.environ["HOME"]
in_path = os.path.join(home, "scratch", "to_coalesce")
out_path = os.path.join(home, "scratch", "coalesced")

os.makedirs(in_path, exist_ok=True)
os.makedirs(out_path, exist_ok=True)

df = pd.read_csv('https://raw.githubusercontent.com/mwaskom/seaborn-data/master/iris.csv')

for i in range(10):
    dfcopy = df.copy()
    dfcopy["file"] = i
    dfcopy.to_parquet(os.path.join(in_path, f"iris_{i}.parquet"))
    
coalese_parquets(in_path, outpath=os.path.join(out_path, "coalesce.parquet"))
print(pq.ParquetFile(os.path.join(out_path, "coalesce.parquet")).metadata)
# <pyarrow._parquet.FileMetaData object at 0x1575f9d60>
#   created_by: parquet-cpp-arrow version 7.0.0
#   num_columns: 6
#   num_rows: 1500
#   num_row_groups: 1
#   format_version: 1.0
#   serialized_size: 3857