diff --git a/dev/provision.py b/dev/provision.py index 5b198ce94b..837189204e 100644 --- a/dev/provision.py +++ b/dev/provision.py @@ -14,6 +14,7 @@ # KIND, either express or implied. See the License for the # specific language governing permissions and limitations # under the License. +import math from pyspark.sql import SparkSession from pyspark.sql.functions import current_date, date_add, expr @@ -113,89 +114,99 @@ """ ) - spark.sql( - f""" - CREATE OR REPLACE TABLE {catalog_name}.default.test_positional_mor_deletes ( - dt date, - number integer, - letter string - ) - USING iceberg - TBLPROPERTIES ( - 'write.delete.mode'='merge-on-read', - 'write.update.mode'='merge-on-read', - 'write.merge.mode'='merge-on-read', - 'format-version'='2' - ); - """ - ) + # Merge on read has been implemented in version ≥2: + # v2: Using positional deletes + # v3: Using deletion vectors - spark.sql( - f""" - INSERT INTO {catalog_name}.default.test_positional_mor_deletes - VALUES - (CAST('2023-03-01' AS date), 1, 'a'), - (CAST('2023-03-02' AS date), 2, 'b'), - (CAST('2023-03-03' AS date), 3, 'c'), - (CAST('2023-03-04' AS date), 4, 'd'), - (CAST('2023-03-05' AS date), 5, 'e'), - (CAST('2023-03-06' AS date), 6, 'f'), - (CAST('2023-03-07' AS date), 7, 'g'), - (CAST('2023-03-08' AS date), 8, 'h'), - (CAST('2023-03-09' AS date), 9, 'i'), - (CAST('2023-03-10' AS date), 10, 'j'), - (CAST('2023-03-11' AS date), 11, 'k'), - (CAST('2023-03-12' AS date), 12, 'l'); - """ - ) + for format_version in [2, 3]: + identifier = f'{catalog_name}.default.test_positional_mor_deletes_v{format_version}' + spark.sql( + f""" + CREATE OR REPLACE TABLE {identifier} ( + dt date, + number integer, + letter string + ) + USING iceberg + TBLPROPERTIES ( + 'write.delete.mode'='merge-on-read', + 'write.update.mode'='merge-on-read', + 'write.merge.mode'='merge-on-read', + 'format-version'='{format_version}' + ); + """ + ) + + spark.sql( + f""" + INSERT INTO {identifier} + VALUES + (CAST('2023-03-01' AS date), 1, 'a'), + (CAST('2023-03-02' AS date), 2, 'b'), + (CAST('2023-03-03' AS date), 3, 'c'), + (CAST('2023-03-04' AS date), 4, 'd'), + (CAST('2023-03-05' AS date), 5, 'e'), + (CAST('2023-03-06' AS date), 6, 'f'), + (CAST('2023-03-07' AS date), 7, 'g'), + (CAST('2023-03-08' AS date), 8, 'h'), + (CAST('2023-03-09' AS date), 9, 'i'), + (CAST('2023-03-10' AS date), 10, 'j'), + (CAST('2023-03-11' AS date), 11, 'k'), + (CAST('2023-03-12' AS date), 12, 'l'); + """ + ) - spark.sql(f"ALTER TABLE {catalog_name}.default.test_positional_mor_deletes CREATE TAG tag_12") + spark.sql(f"ALTER TABLE {identifier} CREATE TAG tag_12") - spark.sql(f"ALTER TABLE {catalog_name}.default.test_positional_mor_deletes CREATE BRANCH without_5") + spark.sql(f"ALTER TABLE {identifier} CREATE BRANCH without_5") - spark.sql(f"DELETE FROM {catalog_name}.default.test_positional_mor_deletes.branch_without_5 WHERE number = 5") + spark.sql(f"DELETE FROM {identifier}.branch_without_5 WHERE number = 5") - spark.sql(f"DELETE FROM {catalog_name}.default.test_positional_mor_deletes WHERE number = 9") + spark.sql(f"DELETE FROM {identifier} WHERE number = 9") - spark.sql( - f""" - CREATE OR REPLACE TABLE {catalog_name}.default.test_positional_mor_double_deletes ( - dt date, - number integer, - letter string - ) - USING iceberg - TBLPROPERTIES ( - 'write.delete.mode'='merge-on-read', - 'write.update.mode'='merge-on-read', - 'write.merge.mode'='merge-on-read', - 'format-version'='2' - ); - """ - ) + identifier = f'{catalog_name}.default.test_positional_mor_double_deletes_v{format_version}' - spark.sql( - f""" - INSERT INTO {catalog_name}.default.test_positional_mor_double_deletes - VALUES - (CAST('2023-03-01' AS date), 1, 'a'), - (CAST('2023-03-02' AS date), 2, 'b'), - (CAST('2023-03-03' AS date), 3, 'c'), - (CAST('2023-03-04' AS date), 4, 'd'), - (CAST('2023-03-05' AS date), 5, 'e'), - (CAST('2023-03-06' AS date), 6, 'f'), - (CAST('2023-03-07' AS date), 7, 'g'), - (CAST('2023-03-08' AS date), 8, 'h'), - (CAST('2023-03-09' AS date), 9, 'i'), - (CAST('2023-03-10' AS date), 10, 'j'), - (CAST('2023-03-11' AS date), 11, 'k'), - (CAST('2023-03-12' AS date), 12, 'l'); - """ - ) + spark.sql( + f""" + CREATE OR REPLACE TABLE {identifier} ( + dt date, + number integer, + letter string + ) + USING iceberg + TBLPROPERTIES ( + 'write.delete.mode'='merge-on-read', + 'write.update.mode'='merge-on-read', + 'write.merge.mode'='merge-on-read', + 'format-version'='2' + ); + """ + ) - spark.sql(f"DELETE FROM {catalog_name}.default.test_positional_mor_double_deletes WHERE number = 9") + spark.sql( + f""" + INSERT INTO {identifier} + VALUES + (CAST('2023-03-01' AS date), 1, 'a'), + (CAST('2023-03-02' AS date), 2, 'b'), + (CAST('2023-03-03' AS date), 3, 'c'), + (CAST('2023-03-04' AS date), 4, 'd'), + (CAST('2023-03-05' AS date), 5, 'e'), + (CAST('2023-03-06' AS date), 6, 'f'), + (CAST('2023-03-07' AS date), 7, 'g'), + (CAST('2023-03-08' AS date), 8, 'h'), + (CAST('2023-03-09' AS date), 9, 'i'), + (CAST('2023-03-10' AS date), 10, 'j'), + (CAST('2023-03-11' AS date), 11, 'k'), + (CAST('2023-03-12' AS date), 12, 'l'); + """ + ) - spark.sql(f"DELETE FROM {catalog_name}.default.test_positional_mor_double_deletes WHERE letter == 'f'") + # Perform two deletes, should produce: + # v2: two positional delete files in v2 + # v3: one deletion vector since they are merged + spark.sql(f"DELETE FROM {identifier} WHERE number = 9") + spark.sql(f"DELETE FROM {identifier} WHERE letter == 'f'") all_types_dataframe = ( spark.range(0, 5, 1, 5) diff --git a/poetry.lock b/poetry.lock index 38872a5030..d9c43b8b34 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.0.1 and should not be changed by hand. [[package]] name = "adlfs" @@ -27,15 +27,15 @@ tests = ["arrow", "dask[dataframe]", "docker", "pytest", "pytest-mock"] [[package]] name = "aiobotocore" -version = "2.21.0" +version = "2.21.1" description = "Async client for aws services using botocore and aiohttp" optional = true python-versions = ">=3.8" groups = ["main"] markers = "extra == \"s3fs\"" files = [ - {file = "aiobotocore-2.21.0-py3-none-any.whl", hash = "sha256:05b4e29690a07913297686d819dc8dac341a5361f14fedf444bdd77ae1e36554"}, - {file = "aiobotocore-2.21.0.tar.gz", hash = "sha256:03d64a41e313ebce76fd7c3e4c854e560032ac5cf71f4d5072616ca6fb9701b5"}, + {file = "aiobotocore-2.21.1-py3-none-any.whl", hash = "sha256:bd7c49a6d6f8a3d9444b0a94417c8da13813b5c7eec1c4f0ec2db7e8ce8f23e7"}, + {file = "aiobotocore-2.21.1.tar.gz", hash = "sha256:010357f43004413e92a9d066bb0db1f241aeb29ffed306e9197061ffc94e6577"}, ] [package.dependencies] @@ -53,107 +53,107 @@ boto3 = ["boto3 (>=1.37.0,<1.37.2)"] [[package]] name = "aiohappyeyeballs" 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optional = true python-versions = "*" groups = ["main"] -markers = "extra == \"hive-kerberos\" or extra == \"hive\"" +markers = "extra == \"hive\" or extra == \"hive-kerberos\"" files = [ {file = "thrift-0.21.0.tar.gz", hash = "sha256:5e6f7c50f936ebfa23e924229afc95eb219f8c8e5a83202dd4a391244803e402"}, ] @@ -5261,7 +5339,7 @@ description = "A lil' TOML parser" optional = false python-versions = ">=3.8" groups = ["dev"] -markers = "python_version <= \"3.10\"" +markers = "python_version < \"3.11\"" files = [ {file = "tomli-2.2.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:678e4fa69e4575eb77d103de3df8a895e1591b48e740211bd1067378c69e8249"}, {file = "tomli-2.2.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:023aa114dd824ade0100497eb2318602af309e5a55595f76b626d6d9f3b7b0a6"}, @@ -5322,16 +5400,19 @@ telegram = ["requests"] [[package]] name = "types-setuptools" -version = "75.8.0.20250210" +version = "76.0.0.20250313" description = "Typing stubs for setuptools" optional = false python-versions = ">=3.9" groups = ["dev"] files = [ - {file = "types_setuptools-75.8.0.20250210-py3-none-any.whl", hash = "sha256:a217d7b4d59be04c29e23d142c959a0f85e71292fd3fc4313f016ca11f0b56dc"}, - {file = "types_setuptools-75.8.0.20250210.tar.gz", hash = "sha256:c1547361b2441f07c94e25dce8a068e18c611593ad4b6fdd727b1a8f5d1fda33"}, + {file = "types_setuptools-76.0.0.20250313-py3-none-any.whl", hash = "sha256:bf454b2a49b8cfd7ebcf5844d4dd5fe4c8666782df1e3663c5866fd51a47460e"}, + {file = "types_setuptools-76.0.0.20250313.tar.gz", hash = "sha256:b2be66f550f95f3cad2a7d46177b273c7e9c80df7d257fa57addbbcfc8126a9e"}, ] +[package.dependencies] +setuptools = "*" + [[package]] name = "typing-extensions" version = "4.12.2" @@ -5343,19 +5424,18 @@ files = [ {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"}, {file = "typing_extensions-4.12.2.tar.gz", hash = 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and platform_python_implementation == \"CPython\"", "brotli (>=1.0.9) ; python_version >= \"3\" and platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; (os_name != \"nt\" or python_version >= \"3\") and platform_python_implementation != \"CPython\"", "brotlipy (>=0.6.0) ; os_name == \"nt\" and python_version < \"3\""] -secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress ; python_version == \"2.7\"", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"] +brotli = ["brotli (==1.0.9)", "brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"] +secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"] socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] @@ -5383,28 +5463,28 @@ description = "HTTP library with thread-safe connection pooling, file post, and optional = false python-versions = ">=3.9" groups = ["main", "dev", "docs"] -markers = "python_version >= \"3.10\"" +markers = "python_version >= \"3.10\" and python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "urllib3-2.3.0-py3-none-any.whl", hash = "sha256:1cee9ad369867bfdbbb48b7dd50374c0967a0bb7710050facf0dd6911440e3df"}, {file = "urllib3-2.3.0.tar.gz", hash = "sha256:f8c5449b3cf0861679ce7e0503c7b44b5ec981bec0d1d3795a07f1ba96f0204d"}, ] [package.extras] -brotli = ["brotli (>=1.0.9) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\""] +brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] h2 = ["h2 (>=4,<5)"] socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] zstd = ["zstandard (>=0.18.0)"] [[package]] name = "virtualenv" -version = "20.29.2" +version = "20.29.3" description = "Virtual Python Environment builder" optional = false python-versions = ">=3.8" groups = ["dev"] files = [ - {file = "virtualenv-20.29.2-py3-none-any.whl", hash = "sha256:febddfc3d1ea571bdb1dc0f98d7b45d24def7428214d4fb73cc486c9568cce6a"}, - {file = "virtualenv-20.29.2.tar.gz", hash = "sha256:fdaabebf6d03b5ba83ae0a02cfe96f48a716f4fae556461d180825866f75b728"}, + {file = "virtualenv-20.29.3-py3-none-any.whl", hash = "sha256:3e3d00f5807e83b234dfb6122bf37cfadf4be216c53a49ac059d02414f819170"}, + {file = "virtualenv-20.29.3.tar.gz", hash = "sha256:95e39403fcf3940ac45bc717597dba16110b74506131845d9b687d5e73d947ac"}, ] [package.dependencies] @@ -5414,7 +5494,7 @@ platformdirs = ">=3.9.1,<5" [package.extras] docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] -test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8) ; platform_python_implementation == \"PyPy\" or platform_python_implementation == \"CPython\" and sys_platform == \"win32\" and python_version >= \"3.13\"", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10) ; platform_python_implementation == \"CPython\""] +test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] [[package]] name = "watchdog" @@ -5586,7 +5666,7 @@ description = "Yet another URL library" optional = true python-versions = ">=3.9" groups = ["main"] -markers = "extra == \"adlfs\" or extra == \"gcsfs\" or extra == \"s3fs\"" +markers = "extra == \"s3fs\" or extra == \"adlfs\" or extra == \"gcsfs\"" files = [ {file = "yarl-1.18.3-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:7df647e8edd71f000a5208fe6ff8c382a1de8edfbccdbbfe649d263de07d8c34"}, {file = "yarl-1.18.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:c69697d3adff5aa4f874b19c0e4ed65180ceed6318ec856ebc423aa5850d84f7"}, @@ -5691,11 +5771,11 @@ files = [ markers = {main = "extra == \"daft\" and python_version < \"3.10\"", dev = "python_full_version < \"3.10.2\"", docs = "python_version < \"3.10\""} [package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] enabler = ["pytest-enabler (>=2.2)"] -test = ["big-O", "importlib-resources ; python_version < \"3.9\"", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] type = ["pytest-mypy"] [[package]] @@ -5836,4 +5916,4 @@ zstandard = ["zstandard"] [metadata] lock-version = "2.1" python-versions = "^3.9.2, !=3.9.7" -content-hash = "73caa2a98420bf7ff90dd00a572742465c1d69e4f2ec548cf0a1893397f2a704" +content-hash = "1772c4ef73bf4d04da928ecd2185db3716191f42e20d72fec2b44ba0a633c607" diff --git a/pyiceberg/io/pyarrow.py b/pyiceberg/io/pyarrow.py index 88be6abac7..9e200aaf67 100644 --- a/pyiceberg/io/pyarrow.py +++ b/pyiceberg/io/pyarrow.py @@ -144,6 +144,7 @@ from pyiceberg.table.locations import load_location_provider from pyiceberg.table.metadata import TableMetadata from pyiceberg.table.name_mapping import NameMapping, apply_name_mapping +from pyiceberg.table.puffin import PuffinFile from pyiceberg.transforms import IdentityTransform, TruncateTransform from pyiceberg.typedef import EMPTY_DICT, Properties, Record from pyiceberg.types import ( @@ -915,15 +916,26 @@ def _construct_fragment(fs: FileSystem, data_file: DataFile, file_format_kwargs: def _read_deletes(fs: FileSystem, data_file: DataFile) -> Dict[str, pa.ChunkedArray]: - delete_fragment = _construct_fragment( - fs, data_file, file_format_kwargs={"dictionary_columns": ("file_path",), "pre_buffer": True, "buffer_size": ONE_MEGABYTE} - ) - table = ds.Scanner.from_fragment(fragment=delete_fragment).to_table() - table = table.unify_dictionaries() - return { - file.as_py(): table.filter(pc.field("file_path") == file).column("pos") - for file in table.column("file_path").chunks[0].dictionary - } + if data_file.file_format == FileFormat.PARQUET: + delete_fragment = _construct_fragment( + fs, + data_file, + file_format_kwargs={"dictionary_columns": ("file_path",), "pre_buffer": True, "buffer_size": ONE_MEGABYTE}, + ) + table = ds.Scanner.from_fragment(fragment=delete_fragment).to_table() + table = table.unify_dictionaries() + return { + file.as_py(): table.filter(pc.field("file_path") == file).column("pos") + for file in table.column("file_path").chunks[0].dictionary + } + elif data_file.file_format == FileFormat.PUFFIN: + _, _, path = PyArrowFileIO.parse_location(data_file.file_path) + with fs.open_input_file(path) as fi: + payload = fi.read() + + return PuffinFile(payload).to_vector() + else: + raise ValueError(f"Delete file format not supported: {data_file.file_format}") def _combine_positional_deletes(positional_deletes: List[pa.ChunkedArray], start_index: int, end_index: int) -> pa.Array: diff --git a/pyiceberg/manifest.py b/pyiceberg/manifest.py index 5a32a6330c..832f7d5b87 100644 --- a/pyiceberg/manifest.py +++ b/pyiceberg/manifest.py @@ -97,6 +97,7 @@ class FileFormat(str, Enum): AVRO = "AVRO" PARQUET = "PARQUET" ORC = "ORC" + PUFFIN = "PUFFIN" @classmethod def _missing_(cls, value: object) -> Union[None, str]: diff --git a/pyiceberg/table/puffin.py b/pyiceberg/table/puffin.py new file mode 100644 index 0000000000..a90ef7ee0d --- /dev/null +++ b/pyiceberg/table/puffin.py @@ -0,0 +1,116 @@ +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. +import math +from typing import TYPE_CHECKING, Dict, List, Literal, Optional + +from pydantic import Field +from pyroaring import BitMap, FrozenBitMap + +from pyiceberg.typedef import IcebergBaseModel + +if TYPE_CHECKING: + import pyarrow as pa + +# Short for: Puffin Fratercula arctica, version 1 +MAGIC_BYTES = b"PFA1" +EMPTY_BITMAP = FrozenBitMap() +MAX_JAVA_SIGNED = int(math.pow(2, 31)) - 1 +PROPERTY_REFERENCED_DATA_FILE = "referenced-data-file" + + +def _deserialize_bitmap(pl: bytes) -> List[BitMap]: + number_of_bitmaps = int.from_bytes(pl[0:8], byteorder="little") + pl = pl[8:] + + bitmaps = [] + last_key = -1 + for _ in range(number_of_bitmaps): + key = int.from_bytes(pl[0:4], byteorder="little") + if key < 0: + raise ValueError(f"Invalid unsigned key: {key}") + if key <= last_key: + raise ValueError("Keys must be sorted in ascending order") + if key > MAX_JAVA_SIGNED: + raise ValueError(f"Key {key} is too large, max {MAX_JAVA_SIGNED} to maintain compatibility with Java impl") + pl = pl[4:] + + while last_key < key - 1: + bitmaps.append(EMPTY_BITMAP) + last_key += 1 + + bm = BitMap().deserialize(pl) + # TODO: Optimize this + pl = pl[len(bm.serialize()) :] + bitmaps.append(bm) + + last_key = key + + return bitmaps + + +class PuffinBlobMetadata(IcebergBaseModel): + type: Literal["deletion-vector-v1"] = Field() + fields: List[int] = Field() + snapshot_id: int = Field(alias="snapshot-id") + sequence_number: int = Field(alias="sequence-number") + offset: int = Field() + length: int = Field() + compression_codec: Optional[str] = Field(alias="compression-codec", default=None) + properties: Dict[str, str] = Field(default_factory=dict) + + +class Footer(IcebergBaseModel): + blobs: List[PuffinBlobMetadata] = Field() + properties: Dict[str, str] = Field(default_factory=dict) + + +def _bitmaps_to_chunked_array(bitmaps: List[BitMap]) -> "pa.ChunkedArray": + import pyarrow as pa + + return pa.chunked_array([(key_pos << 32) + pos for pos in bitmap] for key_pos, bitmap in enumerate(bitmaps)) + + +class PuffinFile: + footer: Footer + _deletion_vectors: Dict[str, List[BitMap]] + + def __init__(self, puffin: bytes) -> None: + for magic_bytes in [puffin[:4], puffin[-4:]]: + if magic_bytes != MAGIC_BYTES: + raise ValueError(f"Incorrect magic bytes, expected {MAGIC_BYTES!r}, got {magic_bytes!r}") + + # One flag is set, the rest should be zero + # byte 0 (first) + # - bit 0 (lowest bit): whether FooterPayload is compressed + # - all other bits are reserved for future use and should be set to 0 on write + flags = puffin[-8:-4] + if flags[0] != 0: + raise ValueError("The Puffin-file has a compressed footer, which is not yet supported") + + # 4 byte integer is always signed, in a two's complement representation, stored little-endian. + footer_payload_size_int = int.from_bytes(puffin[-12:-8], byteorder="little") + + self.footer = Footer.model_validate_json(puffin[-(footer_payload_size_int + 12) : -12]) + puffin = puffin[8:] + + self._deletion_vectors = { + blob.properties[PROPERTY_REFERENCED_DATA_FILE]: _deserialize_bitmap(puffin[blob.offset : blob.offset + blob.length]) + for blob in self.footer.blobs + } + + def to_vector(self) -> Dict[str, "pa.ChunkedArray"]: + return {path: _bitmaps_to_chunked_array(bitmaps) for path, bitmaps in self._deletion_vectors.items()} diff --git a/pyproject.toml b/pyproject.toml index 265dec0ccc..d167686be7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -61,6 +61,7 @@ fsspec = ">=2023.1.0" pyparsing = ">=3.1.0,<4.0.0" zstandard = ">=0.13.0,<1.0.0" tenacity = ">=8.2.3,<10.0.0" +pyroaring = ">=1.0.0,<2.0.0" pyarrow = { version = ">=17.0.0,<20.0.0", optional = true } pandas = { version = ">=1.0.0,<3.0.0", optional = true } duckdb = { version = ">=0.5.0,<2.0.0", optional = true } @@ -509,5 +510,9 @@ ignore_missing_imports = true module = "datafusion.*" ignore_missing_imports = true +[[tool.mypy.overrides]] +module = "pyroaring.*" +ignore_missing_imports = true + [tool.coverage.run] source = ['pyiceberg/'] diff --git a/tests/integration/test_reads.py b/tests/integration/test_reads.py index ab486716de..8ab15489ef 100644 --- a/tests/integration/test_reads.py +++ b/tests/integration/test_reads.py @@ -385,7 +385,8 @@ def test_pyarrow_to_iceberg_all_types(catalog: Catalog) -> None: @pytest.mark.integration @pytest.mark.parametrize("catalog", [pytest.lazy_fixture("session_catalog_hive"), pytest.lazy_fixture("session_catalog")]) -def test_pyarrow_deletes(catalog: Catalog) -> None: +@pytest.mark.parametrize("format_version", [2, 3]) +def test_pyarrow_deletes(catalog: Catalog, format_version: int) -> None: # number, letter # (1, 'a'), # (2, 'b'), @@ -399,7 +400,7 @@ def test_pyarrow_deletes(catalog: Catalog) -> None: # (10, 'j'), # (11, 'k'), # (12, 'l') - test_positional_mor_deletes = catalog.load_table("default.test_positional_mor_deletes") + test_positional_mor_deletes = catalog.load_table(f"default.test_positional_mor_deletes_v{format_version}") arrow_table = test_positional_mor_deletes.scan().to_arrow() assert arrow_table["number"].to_pylist() == [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12] @@ -422,7 +423,8 @@ def test_pyarrow_deletes(catalog: Catalog) -> None: @pytest.mark.integration @pytest.mark.parametrize("catalog", [pytest.lazy_fixture("session_catalog_hive"), pytest.lazy_fixture("session_catalog")]) -def test_pyarrow_deletes_double(catalog: Catalog) -> None: +@pytest.mark.parametrize("format_version", [2, 3]) +def test_pyarrow_deletes_double(catalog: Catalog, format_version: int) -> None: # number, letter # (1, 'a'), # (2, 'b'), @@ -436,7 +438,7 @@ def test_pyarrow_deletes_double(catalog: Catalog) -> None: # (10, 'j'), # (11, 'k'), # (12, 'l') - test_positional_mor_double_deletes = catalog.load_table("default.test_positional_mor_double_deletes") + test_positional_mor_double_deletes = catalog.load_table(f"default.test_positional_mor_double_deletes_v{format_version}") arrow_table = test_positional_mor_double_deletes.scan().to_arrow() assert arrow_table["number"].to_pylist() == [1, 2, 3, 4, 5, 7, 8, 10, 11, 12] @@ -459,7 +461,8 @@ def test_pyarrow_deletes_double(catalog: Catalog) -> None: @pytest.mark.integration @pytest.mark.parametrize("catalog", [pytest.lazy_fixture("session_catalog_hive"), pytest.lazy_fixture("session_catalog")]) -def test_pyarrow_batches_deletes(catalog: Catalog) -> None: +@pytest.mark.parametrize("format_version", [2, 3]) +def test_pyarrow_batches_deletes(catalog: Catalog, format_version: int) -> None: # number, letter # (1, 'a'), # (2, 'b'), @@ -473,7 +476,7 @@ def test_pyarrow_batches_deletes(catalog: Catalog) -> None: # (10, 'j'), # (11, 'k'), # (12, 'l') - test_positional_mor_deletes = catalog.load_table("default.test_positional_mor_deletes") + test_positional_mor_deletes = catalog.load_table(f"default.test_positional_mor_deletes_v{format_version}") arrow_table = test_positional_mor_deletes.scan().to_arrow_batch_reader().read_all() assert arrow_table["number"].to_pylist() == [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12] @@ -500,7 +503,8 @@ def test_pyarrow_batches_deletes(catalog: Catalog) -> None: @pytest.mark.integration @pytest.mark.parametrize("catalog", [pytest.lazy_fixture("session_catalog_hive"), pytest.lazy_fixture("session_catalog")]) -def test_pyarrow_batches_deletes_double(catalog: Catalog) -> None: +@pytest.mark.parametrize("format_version", [2, 3]) +def test_pyarrow_batches_deletes_double(catalog: Catalog, format_version: int) -> None: # number, letter # (1, 'a'), # (2, 'b'), @@ -514,7 +518,7 @@ def test_pyarrow_batches_deletes_double(catalog: Catalog) -> None: # (10, 'j'), # (11, 'k'), # (12, 'l') - test_positional_mor_double_deletes = catalog.load_table("default.test_positional_mor_double_deletes") + test_positional_mor_double_deletes = catalog.load_table(f"default.test_positional_mor_double_deletes_v{format_version}") arrow_table = test_positional_mor_double_deletes.scan().to_arrow_batch_reader().read_all() assert arrow_table["number"].to_pylist() == [1, 2, 3, 4, 5, 7, 8, 10, 11, 12] @@ -596,16 +600,18 @@ def test_unpartitioned_fixed_table(catalog: Catalog) -> None: @pytest.mark.integration @pytest.mark.parametrize("catalog", [pytest.lazy_fixture("session_catalog_hive"), pytest.lazy_fixture("session_catalog")]) -def test_scan_tag(catalog: Catalog) -> None: - test_positional_mor_deletes = catalog.load_table("default.test_positional_mor_deletes") +@pytest.mark.parametrize("format_version", [2, 3]) +def test_scan_tag(catalog: Catalog, format_version: int) -> None: + test_positional_mor_deletes = catalog.load_table(f"default.test_positional_mor_deletes_v{format_version}") arrow_table = test_positional_mor_deletes.scan().use_ref("tag_12").to_arrow() assert arrow_table["number"].to_pylist() == [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12] @pytest.mark.integration @pytest.mark.parametrize("catalog", [pytest.lazy_fixture("session_catalog_hive"), pytest.lazy_fixture("session_catalog")]) -def test_scan_branch(catalog: Catalog) -> None: - test_positional_mor_deletes = catalog.load_table("default.test_positional_mor_deletes") +@pytest.mark.parametrize("format_version", [2, 3]) +def test_scan_branch(catalog: Catalog, format_version: int) -> None: + test_positional_mor_deletes = catalog.load_table(f"default.test_positional_mor_deletes_v{format_version}") arrow_table = test_positional_mor_deletes.scan().use_ref("without_5").to_arrow() assert arrow_table["number"].to_pylist() == [1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12] diff --git a/tests/table/bitmaps/64map32bitvals.bin b/tests/table/bitmaps/64map32bitvals.bin new file mode 100644 index 0000000000..475b894417 Binary files /dev/null and b/tests/table/bitmaps/64map32bitvals.bin differ diff --git a/tests/table/bitmaps/64mapempty.bin b/tests/table/bitmaps/64mapempty.bin new file mode 100644 index 0000000000..1b1cb4d44c Binary files /dev/null and b/tests/table/bitmaps/64mapempty.bin differ diff --git a/tests/table/bitmaps/64maphighvals.bin b/tests/table/bitmaps/64maphighvals.bin new file mode 100644 index 0000000000..d4312b8d22 Binary files /dev/null and b/tests/table/bitmaps/64maphighvals.bin differ diff --git a/tests/table/bitmaps/64mapspreadvals.bin b/tests/table/bitmaps/64mapspreadvals.bin new file mode 100644 index 0000000000..83c72f6ba3 Binary files /dev/null and b/tests/table/bitmaps/64mapspreadvals.bin differ diff --git a/tests/table/test_puffin.py b/tests/table/test_puffin.py new file mode 100644 index 0000000000..2140915389 --- /dev/null +++ b/tests/table/test_puffin.py @@ -0,0 +1,74 @@ +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. +from os import path +from typing import List + +import pytest +from pyroaring import BitMap + +from pyiceberg.table.puffin import _deserialize_bitmap + + +def _open_file(file: str) -> bytes: + cur_dir = path.dirname(path.realpath(__file__)) + with open(f"{cur_dir}/bitmaps/{file}", "rb") as f: + return f.read() + + +def test_map_empty() -> None: + puffin = _open_file("64mapempty.bin") + + expected: List[BitMap] = [] + actual = _deserialize_bitmap(puffin) + + assert expected == actual + + +def test_map_bitvals() -> None: + puffin = _open_file("64map32bitvals.bin") + + expected = [BitMap([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])] + actual = _deserialize_bitmap(puffin) + + assert expected == actual + + +def test_map_spread_vals() -> None: + puffin = _open_file("64mapspreadvals.bin") + + expected = [ + BitMap([0, 1, 2, 3, 4, 5, 6, 7, 8, 9]), + BitMap([0, 1, 2, 3, 4, 5, 6, 7, 8, 9]), + BitMap([0, 1, 2, 3, 4, 5, 6, 7, 8, 9]), + BitMap([0, 1, 2, 3, 4, 5, 6, 7, 8, 9]), + BitMap([0, 1, 2, 3, 4, 5, 6, 7, 8, 9]), + BitMap([0, 1, 2, 3, 4, 5, 6, 7, 8, 9]), + BitMap([0, 1, 2, 3, 4, 5, 6, 7, 8, 9]), + BitMap([0, 1, 2, 3, 4, 5, 6, 7, 8, 9]), + BitMap([0, 1, 2, 3, 4, 5, 6, 7, 8, 9]), + BitMap([0, 1, 2, 3, 4, 5, 6, 7, 8, 9]), + ] + actual = _deserialize_bitmap(puffin) + + assert expected == actual + + +def test_map_high_vals() -> None: + puffin = _open_file("64maphighvals.bin") + + with pytest.raises(ValueError, match="Key 4022190063 is too large, max 2147483647 to maintain compatibility with Java impl"): + _ = _deserialize_bitmap(puffin)