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# 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.
# pylint: disable=redefined-outer-name,arguments-renamed,fixme
"""FileIO implementation for reading and writing table files that uses pyarrow.fs.
This file contains a FileIO implementation that relies on the filesystem interface provided
by PyArrow. It relies on PyArrow's `from_uri` method that infers the correct filesystem
type to use. Theoretically, this allows the supported storage types to grow naturally
with the pyarrow library.
"""
from __future__ import annotations
import concurrent.futures
import fnmatch
import itertools
import logging
import os
import re
from abc import ABC, abstractmethod
from concurrent.futures import Future
from copy import copy
from dataclasses import dataclass
from enum import Enum
from functools import lru_cache, singledispatch
from typing import (
TYPE_CHECKING,
Any,
Callable,
Dict,
Generic,
Iterable,
Iterator,
List,
Optional,
Set,
Tuple,
TypeVar,
Union,
cast,
)
from urllib.parse import urlparse
import numpy as np
import pyarrow as pa
import pyarrow.compute as pc
import pyarrow.dataset as ds
import pyarrow.lib
import pyarrow.parquet as pq
from pyarrow import ChunkedArray
from pyarrow.fs import (
FileInfo,
FileSystem,
FileType,
FSSpecHandler,
)
from sortedcontainers import SortedList
from pyiceberg.conversions import to_bytes
from pyiceberg.exceptions import ResolveError
from pyiceberg.expressions import (
AlwaysTrue,
BooleanExpression,
BoundTerm,
)
from pyiceberg.expressions.literals import Literal
from pyiceberg.expressions.visitors import (
BoundBooleanExpressionVisitor,
bind,
extract_field_ids,
translate_column_names,
)
from pyiceberg.expressions.visitors import visit as boolean_expression_visit
from pyiceberg.io import (
GCS_DEFAULT_LOCATION,
GCS_ENDPOINT,
GCS_TOKEN,
GCS_TOKEN_EXPIRES_AT_MS,
HDFS_HOST,
HDFS_KERB_TICKET,
HDFS_PORT,
HDFS_USER,
S3_ACCESS_KEY_ID,
S3_CONNECT_TIMEOUT,
S3_ENDPOINT,
S3_PROXY_URI,
S3_REGION,
S3_SECRET_ACCESS_KEY,
S3_SESSION_TOKEN,
FileIO,
InputFile,
InputStream,
OutputFile,
OutputStream,
)
from pyiceberg.manifest import (
DataFile,
DataFileContent,
FileFormat,
)
from pyiceberg.partitioning import PartitionField, PartitionSpec, partition_record_value
from pyiceberg.schema import (
PartnerAccessor,
PreOrderSchemaVisitor,
Schema,
SchemaVisitorPerPrimitiveType,
SchemaWithPartnerVisitor,
pre_order_visit,
promote,
prune_columns,
sanitize_column_names,
visit,
visit_with_partner,
)
from pyiceberg.table import PropertyUtil, TableProperties, WriteTask
from pyiceberg.table.metadata import TableMetadata
from pyiceberg.table.name_mapping import NameMapping
from pyiceberg.transforms import TruncateTransform
from pyiceberg.typedef import EMPTY_DICT, Properties, Record
from pyiceberg.types import (
BinaryType,
BooleanType,
DateType,
DecimalType,
DoubleType,
FixedType,
FloatType,
IcebergType,
IntegerType,
ListType,
LongType,
MapType,
NestedField,
PrimitiveType,
StringType,
StructType,
TimestampType,
TimestamptzType,
TimeType,
UUIDType,
)
from pyiceberg.utils.concurrent import ExecutorFactory
from pyiceberg.utils.datetime import millis_to_datetime
from pyiceberg.utils.singleton import Singleton
from pyiceberg.utils.truncate import truncate_upper_bound_binary_string, truncate_upper_bound_text_string
if TYPE_CHECKING:
from pyiceberg.table import FileScanTask
logger = logging.getLogger(__name__)
ONE_MEGABYTE = 1024 * 1024
BUFFER_SIZE = "buffer-size"
ICEBERG_SCHEMA = b"iceberg.schema"
# The PARQUET: in front means that it is Parquet specific, in this case the field_id
PYARROW_PARQUET_FIELD_ID_KEY = b"PARQUET:field_id"
PYARROW_FIELD_DOC_KEY = b"doc"
LIST_ELEMENT_NAME = "element"
MAP_KEY_NAME = "key"
MAP_VALUE_NAME = "value"
DOC = "doc"
T = TypeVar("T")
class PyArrowLocalFileSystem(pyarrow.fs.LocalFileSystem):
def open_output_stream(self, path: str, *args: Any, **kwargs: Any) -> pyarrow.NativeFile:
# In LocalFileSystem, parent directories must be first created before opening an output stream
self.create_dir(os.path.dirname(path), recursive=True)
return super().open_output_stream(path, *args, **kwargs)
class PyArrowFile(InputFile, OutputFile):
"""A combined InputFile and OutputFile implementation that uses a pyarrow filesystem to generate pyarrow.lib.NativeFile instances.
Args:
location (str): A URI or a path to a local file.
Attributes:
location(str): The URI or path to a local file for a PyArrowFile instance.
Examples:
>>> from pyiceberg.io.pyarrow import PyArrowFile
>>> # input_file = PyArrowFile("s3://foo/bar.txt")
>>> # Read the contents of the PyArrowFile instance
>>> # Make sure that you have permissions to read/write
>>> # file_content = input_file.open().read()
>>> # output_file = PyArrowFile("s3://baz/qux.txt")
>>> # Write bytes to a file
>>> # Make sure that you have permissions to read/write
>>> # output_file.create().write(b'foobytes')
"""
_filesystem: FileSystem
_path: str
_buffer_size: int
def __init__(self, location: str, path: str, fs: FileSystem, buffer_size: int = ONE_MEGABYTE):
self._filesystem = fs
self._path = path
self._buffer_size = buffer_size
super().__init__(location=location)
def _file_info(self) -> FileInfo:
"""Retrieve a pyarrow.fs.FileInfo object for the location.
Raises:
PermissionError: If the file at self.location cannot be accessed due to a permission error such as
an AWS error code 15.
"""
try:
file_info = self._filesystem.get_file_info(self._path)
except OSError as e:
if e.errno == 13 or "AWS Error [code 15]" in str(e):
raise PermissionError(f"Cannot get file info, access denied: {self.location}") from e
raise # pragma: no cover - If some other kind of OSError, raise the raw error
if file_info.type == FileType.NotFound:
raise FileNotFoundError(f"Cannot get file info, file not found: {self.location}")
return file_info
def __len__(self) -> int:
"""Return the total length of the file, in bytes."""
file_info = self._file_info()
return file_info.size
def exists(self) -> bool:
"""Check whether the location exists."""
try:
self._file_info() # raises FileNotFoundError if it does not exist
return True
except FileNotFoundError:
return False
def open(self, seekable: bool = True) -> InputStream:
"""Open the location using a PyArrow FileSystem inferred from the location.
Args:
seekable: If the stream should support seek, or if it is consumed sequential.
Returns:
pyarrow.lib.NativeFile: A NativeFile instance for the file located at `self.location`.
Raises:
FileNotFoundError: If the file at self.location does not exist.
PermissionError: If the file at self.location cannot be accessed due to a permission error such as
an AWS error code 15.
"""
try:
if seekable:
input_file = self._filesystem.open_input_file(self._path)
else:
input_file = self._filesystem.open_input_stream(self._path, buffer_size=self._buffer_size)
except FileNotFoundError:
raise
except PermissionError:
raise
except OSError as e:
if e.errno == 2 or "Path does not exist" in str(e):
raise FileNotFoundError(f"Cannot open file, does not exist: {self.location}") from e
elif e.errno == 13 or "AWS Error [code 15]" in str(e):
raise PermissionError(f"Cannot open file, access denied: {self.location}") from e
raise # pragma: no cover - If some other kind of OSError, raise the raw error
return input_file
def create(self, overwrite: bool = False) -> OutputStream:
"""Create a writable pyarrow.lib.NativeFile for this PyArrowFile's location.
Args:
overwrite (bool): Whether to overwrite the file if it already exists.
Returns:
pyarrow.lib.NativeFile: A NativeFile instance for the file located at self.location.
Raises:
FileExistsError: If the file already exists at `self.location` and `overwrite` is False.
Note:
This retrieves a pyarrow NativeFile by opening an output stream. If overwrite is set to False,
a check is first performed to verify that the file does not exist. This is not thread-safe and
a possibility does exist that the file can be created by a concurrent process after the existence
check yet before the output stream is created. In such a case, the default pyarrow behavior will
truncate the contents of the existing file when opening the output stream.
"""
try:
if not overwrite and self.exists() is True:
raise FileExistsError(f"Cannot create file, already exists: {self.location}")
output_file = self._filesystem.open_output_stream(self._path, buffer_size=self._buffer_size)
except PermissionError:
raise
except OSError as e:
if e.errno == 13 or "AWS Error [code 15]" in str(e):
raise PermissionError(f"Cannot create file, access denied: {self.location}") from e
raise # pragma: no cover - If some other kind of OSError, raise the raw error
return output_file
def to_input_file(self) -> PyArrowFile:
"""Return a new PyArrowFile for the location of an existing PyArrowFile instance.
This method is included to abide by the OutputFile abstract base class. Since this implementation uses a single
PyArrowFile class (as opposed to separate InputFile and OutputFile implementations), this method effectively returns
a copy of the same instance.
"""
return self
class PyArrowFileIO(FileIO):
fs_by_scheme: Callable[[str, Optional[str]], FileSystem]
def __init__(self, properties: Properties = EMPTY_DICT):
self.fs_by_scheme: Callable[[str, Optional[str]], FileSystem] = lru_cache(self._initialize_fs)
super().__init__(properties=properties)
@staticmethod
def parse_location(location: str) -> Tuple[str, str, str]:
"""Return the path without the scheme."""
uri = urlparse(location)
if not uri.scheme:
return "file", uri.netloc, os.path.abspath(location)
elif uri.scheme in ("hdfs", "viewfs"):
return uri.scheme, uri.netloc, uri.path
else:
return uri.scheme, uri.netloc, f"{uri.netloc}{uri.path}"
def _initialize_fs(self, scheme: str, netloc: Optional[str] = None) -> FileSystem:
if scheme in {"s3", "s3a", "s3n"}:
from pyarrow.fs import S3FileSystem
client_kwargs: Dict[str, Any] = {
"endpoint_override": self.properties.get(S3_ENDPOINT),
"access_key": self.properties.get(S3_ACCESS_KEY_ID),
"secret_key": self.properties.get(S3_SECRET_ACCESS_KEY),
"session_token": self.properties.get(S3_SESSION_TOKEN),
"region": self.properties.get(S3_REGION),
}
if proxy_uri := self.properties.get(S3_PROXY_URI):
client_kwargs["proxy_options"] = proxy_uri
if connect_timeout := self.properties.get(S3_CONNECT_TIMEOUT):
client_kwargs["connect_timeout"] = float(connect_timeout)
return S3FileSystem(**client_kwargs)
elif scheme in ("hdfs", "viewfs"):
from pyarrow.fs import HadoopFileSystem
hdfs_kwargs: Dict[str, Any] = {}
if netloc:
return HadoopFileSystem.from_uri(f"{scheme}://{netloc}")
if host := self.properties.get(HDFS_HOST):
hdfs_kwargs["host"] = host
if port := self.properties.get(HDFS_PORT):
# port should be an integer type
hdfs_kwargs["port"] = int(port)
if user := self.properties.get(HDFS_USER):
hdfs_kwargs["user"] = user
if kerb_ticket := self.properties.get(HDFS_KERB_TICKET):
hdfs_kwargs["kerb_ticket"] = kerb_ticket
return HadoopFileSystem(**hdfs_kwargs)
elif scheme in {"gs", "gcs"}:
from pyarrow.fs import GcsFileSystem
gcs_kwargs: Dict[str, Any] = {}
if access_token := self.properties.get(GCS_TOKEN):
gcs_kwargs["access_token"] = access_token
if expiration := self.properties.get(GCS_TOKEN_EXPIRES_AT_MS):
gcs_kwargs["credential_token_expiration"] = millis_to_datetime(int(expiration))
if bucket_location := self.properties.get(GCS_DEFAULT_LOCATION):
gcs_kwargs["default_bucket_location"] = bucket_location
if endpoint := self.properties.get(GCS_ENDPOINT):
url_parts = urlparse(endpoint)
gcs_kwargs["scheme"] = url_parts.scheme
gcs_kwargs["endpoint_override"] = url_parts.netloc
return GcsFileSystem(**gcs_kwargs)
elif scheme == "file":
return PyArrowLocalFileSystem()
else:
raise ValueError(f"Unrecognized filesystem type in URI: {scheme}")
def new_input(self, location: str) -> PyArrowFile:
"""Get a PyArrowFile instance to read bytes from the file at the given location.
Args:
location (str): A URI or a path to a local file.
Returns:
PyArrowFile: A PyArrowFile instance for the given location.
"""
scheme, netloc, path = self.parse_location(location)
return PyArrowFile(
fs=self.fs_by_scheme(scheme, netloc),
location=location,
path=path,
buffer_size=int(self.properties.get(BUFFER_SIZE, ONE_MEGABYTE)),
)
def new_output(self, location: str) -> PyArrowFile:
"""Get a PyArrowFile instance to write bytes to the file at the given location.
Args:
location (str): A URI or a path to a local file.
Returns:
PyArrowFile: A PyArrowFile instance for the given location.
"""
scheme, netloc, path = self.parse_location(location)
return PyArrowFile(
fs=self.fs_by_scheme(scheme, netloc),
location=location,
path=path,
buffer_size=int(self.properties.get(BUFFER_SIZE, ONE_MEGABYTE)),
)
def delete(self, location: Union[str, InputFile, OutputFile]) -> None:
"""Delete the file at the given location.
Args:
location (Union[str, InputFile, OutputFile]): The URI to the file--if an InputFile instance or an OutputFile instance is provided,
the location attribute for that instance is used as the location to delete.
Raises:
FileNotFoundError: When the file at the provided location does not exist.
PermissionError: If the file at the provided location cannot be accessed due to a permission error such as
an AWS error code 15.
"""
str_location = location.location if isinstance(location, (InputFile, OutputFile)) else location
scheme, netloc, path = self.parse_location(str_location)
fs = self.fs_by_scheme(scheme, netloc)
try:
fs.delete_file(path)
except FileNotFoundError:
raise
except PermissionError:
raise
except OSError as e:
if e.errno == 2 or "Path does not exist" in str(e):
raise FileNotFoundError(f"Cannot delete file, does not exist: {location}") from e
elif e.errno == 13 or "AWS Error [code 15]" in str(e):
raise PermissionError(f"Cannot delete file, access denied: {location}") from e
raise # pragma: no cover - If some other kind of OSError, raise the raw error
def __getstate__(self) -> Dict[str, Any]:
"""Create a dictionary of the PyArrowFileIO fields used when pickling."""
fileio_copy = copy(self.__dict__)
fileio_copy["fs_by_scheme"] = None
return fileio_copy
def __setstate__(self, state: Dict[str, Any]) -> None:
"""Deserialize the state into a PyArrowFileIO instance."""
self.__dict__ = state
self.fs_by_scheme = lru_cache(self._initialize_fs)
def schema_to_pyarrow(
schema: Union[Schema, IcebergType], metadata: Dict[bytes, bytes] = EMPTY_DICT, include_field_ids: bool = True
) -> pa.schema:
return visit(schema, _ConvertToArrowSchema(metadata, include_field_ids))
class _ConvertToArrowSchema(SchemaVisitorPerPrimitiveType[pa.DataType]):
_metadata: Dict[bytes, bytes]
def __init__(self, metadata: Dict[bytes, bytes] = EMPTY_DICT, include_field_ids: bool = True) -> None:
self._metadata = metadata
self._include_field_ids = include_field_ids
def schema(self, _: Schema, struct_result: pa.StructType) -> pa.schema:
return pa.schema(list(struct_result), metadata=self._metadata)
def struct(self, _: StructType, field_results: List[pa.DataType]) -> pa.DataType:
return pa.struct(field_results)
def field(self, field: NestedField, field_result: pa.DataType) -> pa.Field:
metadata = {}
if field.doc:
metadata[PYARROW_FIELD_DOC_KEY] = field.doc
if self._include_field_ids:
metadata[PYARROW_PARQUET_FIELD_ID_KEY] = str(field.field_id)
return pa.field(
name=field.name,
type=field_result,
nullable=field.optional,
metadata=metadata,
)
def list(self, list_type: ListType, element_result: pa.DataType) -> pa.DataType:
element_field = self.field(list_type.element_field, element_result)
return pa.list_(value_type=element_field)
def map(self, map_type: MapType, key_result: pa.DataType, value_result: pa.DataType) -> pa.DataType:
key_field = self.field(map_type.key_field, key_result)
value_field = self.field(map_type.value_field, value_result)
return pa.map_(key_type=key_field, item_type=value_field)
def visit_fixed(self, fixed_type: FixedType) -> pa.DataType:
return pa.binary(len(fixed_type))
def visit_decimal(self, decimal_type: DecimalType) -> pa.DataType:
return pa.decimal128(decimal_type.precision, decimal_type.scale)
def visit_boolean(self, _: BooleanType) -> pa.DataType:
return pa.bool_()
def visit_integer(self, _: IntegerType) -> pa.DataType:
return pa.int32()
def visit_long(self, _: LongType) -> pa.DataType:
return pa.int64()
def visit_float(self, _: FloatType) -> pa.DataType:
# 32-bit IEEE 754 floating point
return pa.float32()
def visit_double(self, _: DoubleType) -> pa.DataType:
# 64-bit IEEE 754 floating point
return pa.float64()
def visit_date(self, _: DateType) -> pa.DataType:
# Date encoded as an int
return pa.date32()
def visit_time(self, _: TimeType) -> pa.DataType:
return pa.time64("us")
def visit_timestamp(self, _: TimestampType) -> pa.DataType:
return pa.timestamp(unit="us")
def visit_timestamptz(self, _: TimestamptzType) -> pa.DataType:
return pa.timestamp(unit="us", tz="UTC")
def visit_string(self, _: StringType) -> pa.DataType:
return pa.string()
def visit_uuid(self, _: UUIDType) -> pa.DataType:
return pa.binary(16)
def visit_binary(self, _: BinaryType) -> pa.DataType:
return pa.large_binary()
def _convert_scalar(value: Any, iceberg_type: IcebergType) -> pa.scalar:
if not isinstance(iceberg_type, PrimitiveType):
raise ValueError(f"Expected primitive type, got: {iceberg_type}")
return pa.scalar(value=value, type=schema_to_pyarrow(iceberg_type))
class _ConvertToArrowExpression(BoundBooleanExpressionVisitor[pc.Expression]):
def visit_in(self, term: BoundTerm[pc.Expression], literals: Set[Any]) -> pc.Expression:
pyarrow_literals = pa.array(literals, type=schema_to_pyarrow(term.ref().field.field_type))
return pc.field(term.ref().field.name).isin(pyarrow_literals)
def visit_not_in(self, term: BoundTerm[pc.Expression], literals: Set[Any]) -> pc.Expression:
pyarrow_literals = pa.array(literals, type=schema_to_pyarrow(term.ref().field.field_type))
return ~pc.field(term.ref().field.name).isin(pyarrow_literals)
def visit_is_nan(self, term: BoundTerm[Any]) -> pc.Expression:
ref = pc.field(term.ref().field.name)
return pc.is_nan(ref)
def visit_not_nan(self, term: BoundTerm[Any]) -> pc.Expression:
ref = pc.field(term.ref().field.name)
return ~pc.is_nan(ref)
def visit_is_null(self, term: BoundTerm[Any]) -> pc.Expression:
return pc.field(term.ref().field.name).is_null(nan_is_null=False)
def visit_not_null(self, term: BoundTerm[Any]) -> pc.Expression:
return pc.field(term.ref().field.name).is_valid()
def visit_equal(self, term: BoundTerm[Any], literal: Literal[Any]) -> pc.Expression:
return pc.field(term.ref().field.name) == _convert_scalar(literal.value, term.ref().field.field_type)
def visit_not_equal(self, term: BoundTerm[Any], literal: Literal[Any]) -> pc.Expression:
return pc.field(term.ref().field.name) != _convert_scalar(literal.value, term.ref().field.field_type)
def visit_greater_than_or_equal(self, term: BoundTerm[Any], literal: Literal[Any]) -> pc.Expression:
return pc.field(term.ref().field.name) >= _convert_scalar(literal.value, term.ref().field.field_type)
def visit_greater_than(self, term: BoundTerm[Any], literal: Literal[Any]) -> pc.Expression:
return pc.field(term.ref().field.name) > _convert_scalar(literal.value, term.ref().field.field_type)
def visit_less_than(self, term: BoundTerm[Any], literal: Literal[Any]) -> pc.Expression:
return pc.field(term.ref().field.name) < _convert_scalar(literal.value, term.ref().field.field_type)
def visit_less_than_or_equal(self, term: BoundTerm[Any], literal: Literal[Any]) -> pc.Expression:
return pc.field(term.ref().field.name) <= _convert_scalar(literal.value, term.ref().field.field_type)
def visit_starts_with(self, term: BoundTerm[Any], literal: Literal[Any]) -> pc.Expression:
return pc.starts_with(pc.field(term.ref().field.name), literal.value)
def visit_not_starts_with(self, term: BoundTerm[Any], literal: Literal[Any]) -> pc.Expression:
return ~pc.starts_with(pc.field(term.ref().field.name), literal.value)
def visit_true(self) -> pc.Expression:
return pc.scalar(True)
def visit_false(self) -> pc.Expression:
return pc.scalar(False)
def visit_not(self, child_result: pc.Expression) -> pc.Expression:
return ~child_result
def visit_and(self, left_result: pc.Expression, right_result: pc.Expression) -> pc.Expression:
return left_result & right_result
def visit_or(self, left_result: pc.Expression, right_result: pc.Expression) -> pc.Expression:
return left_result | right_result
def expression_to_pyarrow(expr: BooleanExpression) -> pc.Expression:
return boolean_expression_visit(expr, _ConvertToArrowExpression())
@lru_cache
def _get_file_format(file_format: FileFormat, **kwargs: Dict[str, Any]) -> ds.FileFormat:
if file_format == FileFormat.PARQUET:
return ds.ParquetFileFormat(**kwargs)
else:
raise ValueError(f"Unsupported file format: {file_format}")
def _construct_fragment(fs: FileSystem, data_file: DataFile, file_format_kwargs: Dict[str, Any] = EMPTY_DICT) -> ds.Fragment:
_, _, path = PyArrowFileIO.parse_location(data_file.file_path)
return _get_file_format(data_file.file_format, **file_format_kwargs).make_fragment(path, fs)
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
}
def _combine_positional_deletes(positional_deletes: List[pa.ChunkedArray], rows: int) -> pa.Array:
if len(positional_deletes) == 1:
all_chunks = positional_deletes[0]
else:
all_chunks = pa.chunked_array(itertools.chain(*[arr.chunks for arr in positional_deletes]))
return np.setdiff1d(np.arange(rows), all_chunks, assume_unique=False)
def pyarrow_to_schema(schema: pa.Schema, name_mapping: Optional[NameMapping] = None) -> Schema:
has_ids = visit_pyarrow(schema, _HasIds())
if has_ids:
visitor = _ConvertToIceberg()
elif name_mapping is not None:
visitor = _ConvertToIceberg(name_mapping=name_mapping)
else:
raise ValueError(
"Parquet file does not have field-ids and the Iceberg table does not have 'schema.name-mapping.default' defined"
)
return visit_pyarrow(schema, visitor)
def _pyarrow_to_schema_without_ids(schema: pa.Schema) -> Schema:
return visit_pyarrow(schema, _ConvertToIcebergWithoutIDs())
@singledispatch
def visit_pyarrow(obj: Union[pa.DataType, pa.Schema], visitor: PyArrowSchemaVisitor[T]) -> T:
"""Apply a pyarrow schema visitor to any point within a schema.
The function traverses the schema in post-order fashion.
Args:
obj (Union[pa.DataType, pa.Schema]): An instance of a Schema or an IcebergType.
visitor (PyArrowSchemaVisitor[T]): An instance of an implementation of the generic PyarrowSchemaVisitor base class.
Raises:
NotImplementedError: If attempting to visit an unrecognized object type.
"""
raise NotImplementedError(f"Cannot visit non-type: {obj}")
@visit_pyarrow.register(pa.Schema)
def _(obj: pa.Schema, visitor: PyArrowSchemaVisitor[T]) -> T:
return visitor.schema(obj, visit_pyarrow(pa.struct(obj), visitor))
@visit_pyarrow.register(pa.StructType)
def _(obj: pa.StructType, visitor: PyArrowSchemaVisitor[T]) -> T:
results = []
for field in obj:
visitor.before_field(field)
result = visit_pyarrow(field.type, visitor)
results.append(visitor.field(field, result))
visitor.after_field(field)
return visitor.struct(obj, results)
@visit_pyarrow.register(pa.ListType)
@visit_pyarrow.register(pa.FixedSizeListType)
@visit_pyarrow.register(pa.LargeListType)
def _(obj: Union[pa.ListType, pa.LargeListType, pa.FixedSizeListType], visitor: PyArrowSchemaVisitor[T]) -> T:
visitor.before_list_element(obj.value_field)
result = visit_pyarrow(obj.value_type, visitor)
visitor.after_list_element(obj.value_field)
return visitor.list(obj, result)
@visit_pyarrow.register(pa.MapType)
def _(obj: pa.MapType, visitor: PyArrowSchemaVisitor[T]) -> T:
visitor.before_map_key(obj.key_field)
key_result = visit_pyarrow(obj.key_type, visitor)
visitor.after_map_key(obj.key_field)
visitor.before_map_value(obj.item_field)
value_result = visit_pyarrow(obj.item_type, visitor)
visitor.after_map_value(obj.item_field)
return visitor.map(obj, key_result, value_result)
@visit_pyarrow.register(pa.DictionaryType)
def _(obj: pa.DictionaryType, visitor: PyArrowSchemaVisitor[T]) -> T:
# Parquet has no dictionary type. dictionary-encoding is handled
# as an encoding detail, not as a separate type.
# We will follow this approach in determining the Iceberg Type,
# as we only support parquet in PyIceberg for now.
logger.warning(f"Iceberg does not have a dictionary type. {type(obj)} will be inferred as {obj.value_type} on read.")
return visit_pyarrow(obj.value_type, visitor)
@visit_pyarrow.register(pa.DataType)
def _(obj: pa.DataType, visitor: PyArrowSchemaVisitor[T]) -> T:
if pa.types.is_nested(obj):
raise TypeError(f"Expected primitive type, got: {type(obj)}")
return visitor.primitive(obj)
class PyArrowSchemaVisitor(Generic[T], ABC):
def before_field(self, field: pa.Field) -> None:
"""Override this method to perform an action immediately before visiting a field."""
def after_field(self, field: pa.Field) -> None:
"""Override this method to perform an action immediately after visiting a field."""
def before_list_element(self, element: pa.Field) -> None:
"""Override this method to perform an action immediately before visiting an element within a ListType."""
def after_list_element(self, element: pa.Field) -> None:
"""Override this method to perform an action immediately after visiting an element within a ListType."""
def before_map_key(self, key: pa.Field) -> None:
"""Override this method to perform an action immediately before visiting a key within a MapType."""
def after_map_key(self, key: pa.Field) -> None:
"""Override this method to perform an action immediately after visiting a key within a MapType."""
def before_map_value(self, value: pa.Field) -> None:
"""Override this method to perform an action immediately before visiting a value within a MapType."""
def after_map_value(self, value: pa.Field) -> None:
"""Override this method to perform an action immediately after visiting a value within a MapType."""
@abstractmethod
def schema(self, schema: pa.Schema, struct_result: T) -> T:
"""Visit a schema."""
@abstractmethod
def struct(self, struct: pa.StructType, field_results: List[T]) -> T:
"""Visit a struct."""
@abstractmethod
def field(self, field: pa.Field, field_result: T) -> T:
"""Visit a field."""
@abstractmethod
def list(self, list_type: pa.ListType, element_result: T) -> T:
"""Visit a list."""
@abstractmethod
def map(self, map_type: pa.MapType, key_result: T, value_result: T) -> T:
"""Visit a map."""
@abstractmethod
def primitive(self, primitive: pa.DataType) -> T:
"""Visit a primitive type."""
def _get_field_id(field: pa.Field) -> Optional[int]:
return (
int(field_id_str.decode())
if (field.metadata and (field_id_str := field.metadata.get(PYARROW_PARQUET_FIELD_ID_KEY)))
else None
)
class _HasIds(PyArrowSchemaVisitor[bool]):
def schema(self, schema: pa.Schema, struct_result: bool) -> bool:
return struct_result
def struct(self, struct: pa.StructType, field_results: List[bool]) -> bool:
return all(field_results)
def field(self, field: pa.Field, field_result: bool) -> bool:
return all([_get_field_id(field) is not None, field_result])
def list(self, list_type: pa.ListType, element_result: bool) -> bool:
element_field = list_type.value_field
element_id = _get_field_id(element_field)
return element_result and element_id is not None
def map(self, map_type: pa.MapType, key_result: bool, value_result: bool) -> bool:
key_field = map_type.key_field
key_id = _get_field_id(key_field)
value_field = map_type.item_field
value_id = _get_field_id(value_field)
return all([key_id is not None, value_id is not None, key_result, value_result])
def primitive(self, primitive: pa.DataType) -> bool:
return True
class _ConvertToIceberg(PyArrowSchemaVisitor[Union[IcebergType, Schema]]):
"""Converts PyArrowSchema to Iceberg Schema. Applies the IDs from name_mapping if provided."""
_field_names: List[str]
_name_mapping: Optional[NameMapping]
def __init__(self, name_mapping: Optional[NameMapping] = None) -> None:
self._field_names = []
self._name_mapping = name_mapping
def _field_id(self, field: pa.Field) -> int:
if self._name_mapping:
return self._name_mapping.find(*self._field_names).field_id
elif (field_id := _get_field_id(field)) is not None:
return field_id
else:
raise ValueError(f"Cannot convert {field} to Iceberg Field as field_id is empty.")
def schema(self, schema: pa.Schema, struct_result: StructType) -> Schema:
return Schema(*struct_result.fields)
def struct(self, struct: pa.StructType, field_results: List[NestedField]) -> StructType:
return StructType(*field_results)
def field(self, field: pa.Field, field_result: IcebergType) -> NestedField:
field_id = self._field_id(field)
field_doc = doc_str.decode() if (field.metadata and (doc_str := field.metadata.get(PYARROW_FIELD_DOC_KEY))) else None
field_type = field_result
return NestedField(field_id, field.name, field_type, required=not field.nullable, doc=field_doc)
def list(self, list_type: pa.ListType, element_result: IcebergType) -> ListType:
element_field = list_type.value_field
self._field_names.append(LIST_ELEMENT_NAME)
element_id = self._field_id(element_field)
self._field_names.pop()
return ListType(element_id, element_result, element_required=not element_field.nullable)
def map(self, map_type: pa.MapType, key_result: IcebergType, value_result: IcebergType) -> MapType:
key_field = map_type.key_field
self._field_names.append(MAP_KEY_NAME)
key_id = self._field_id(key_field)
self._field_names.pop()
value_field = map_type.item_field
self._field_names.append(MAP_VALUE_NAME)
value_id = self._field_id(value_field)
self._field_names.pop()
return MapType(key_id, key_result, value_id, value_result, value_required=not value_field.nullable)
def primitive(self, primitive: pa.DataType) -> PrimitiveType:
if pa.types.is_boolean(primitive):
return BooleanType()
elif pa.types.is_integer(primitive):
width = primitive.bit_width
if width <= 32:
return IntegerType()
elif width <= 64:
return LongType()
else:
# Does not exist (yet)
raise TypeError(f"Unsupported integer type: {primitive}")
elif pa.types.is_float32(primitive):
return FloatType()
elif pa.types.is_float64(primitive):
return DoubleType()
elif isinstance(primitive, pa.Decimal128Type):
primitive = cast(pa.Decimal128Type, primitive)
return DecimalType(primitive.precision, primitive.scale)
elif pa.types.is_string(primitive) or pa.types.is_large_string(primitive):
return StringType()
elif pa.types.is_date32(primitive):
return DateType()
elif isinstance(primitive, pa.Time64Type) and primitive.unit == "us":
return TimeType()
elif pa.types.is_timestamp(primitive):
primitive = cast(pa.TimestampType, primitive)
if primitive.unit == "us":
if primitive.tz == "UTC" or primitive.tz == "+00:00":
return TimestamptzType()
elif primitive.tz is None:
return TimestampType()
elif pa.types.is_binary(primitive) or pa.types.is_large_binary(primitive):
return BinaryType()
elif pa.types.is_fixed_size_binary(primitive):
primitive = cast(pa.FixedSizeBinaryType, primitive)
return FixedType(primitive.byte_width)
raise TypeError(f"Unsupported type: {primitive}")
def before_field(self, field: pa.Field) -> None:
self._field_names.append(field.name)
def after_field(self, field: pa.Field) -> None:
self._field_names.pop()
def before_list_element(self, element: pa.Field) -> None:
self._field_names.append(LIST_ELEMENT_NAME)
def after_list_element(self, element: pa.Field) -> None:
self._field_names.pop()
def before_map_key(self, key: pa.Field) -> None:
self._field_names.append(MAP_KEY_NAME)
def after_map_key(self, element: pa.Field) -> None:
self._field_names.pop()
def before_map_value(self, value: pa.Field) -> None:
self._field_names.append(MAP_VALUE_NAME)
def after_map_value(self, element: pa.Field) -> None:
self._field_names.pop()
class _ConvertToIcebergWithoutIDs(_ConvertToIceberg):
"""
Converts PyArrowSchema to Iceberg Schema with all -1 ids.
The schema generated through this visitor should always be
used in conjunction with `new_table_metadata` function to
assign new field ids in order. This is currently used only
when creating an Iceberg Schema from a PyArrow schema when
creating a new Iceberg table.
"""
def _field_id(self, field: pa.Field) -> int:
return -1
def _task_to_table(
fs: FileSystem,
task: FileScanTask,
bound_row_filter: BooleanExpression,
projected_schema: Schema,
projected_field_ids: Set[int],
positional_deletes: Optional[List[ChunkedArray]],
case_sensitive: bool,
limit: Optional[int] = None,
name_mapping: Optional[NameMapping] = None,
) -> Optional[pa.Table]:
_, _, path = PyArrowFileIO.parse_location(task.file.file_path)
arrow_format = ds.ParquetFileFormat(pre_buffer=True, buffer_size=(ONE_MEGABYTE * 8))
with fs.open_input_file(path) as fin:
fragment = arrow_format.make_fragment(fin)
physical_schema = fragment.physical_schema
file_schema = pyarrow_to_schema(physical_schema, name_mapping)
pyarrow_filter = None
if bound_row_filter is not AlwaysTrue():
translated_row_filter = translate_column_names(bound_row_filter, file_schema, case_sensitive=case_sensitive)
bound_file_filter = bind(file_schema, translated_row_filter, case_sensitive=case_sensitive)
pyarrow_filter = expression_to_pyarrow(bound_file_filter)
file_project_schema = prune_columns(file_schema, projected_field_ids, select_full_types=False)
if file_schema is None:
raise ValueError(f"Missing Iceberg schema in Metadata for file: {path}")
fragment_scanner = ds.Scanner.from_fragment(
fragment=fragment,
schema=physical_schema,
# This will push down the query to Arrow.
# But in case there are positional deletes, we have to apply them first
filter=pyarrow_filter if not positional_deletes else None,
columns=[col.name for col in file_project_schema.columns],
)
if positional_deletes:
# Create the mask of indices that we're interested in
indices = _combine_positional_deletes(positional_deletes, fragment.count_rows())
if limit:
if pyarrow_filter is not None:
# In case of the filter, we don't exactly know how many rows
# we need to fetch upfront, can be optimized in the future:
# https://github.com/apache/arrow/issues/35301
arrow_table = fragment_scanner.take(indices)
arrow_table = arrow_table.filter(pyarrow_filter)
arrow_table = arrow_table.slice(0, limit)
else:
arrow_table = fragment_scanner.take(indices[0:limit])
else:
arrow_table = fragment_scanner.take(indices)
# Apply the user filter
if pyarrow_filter is not None:
arrow_table = arrow_table.filter(pyarrow_filter)
else:
# If there are no deletes, we can just take the head
# and the user-filter is already applied
if limit:
arrow_table = fragment_scanner.head(limit)
else:
arrow_table = fragment_scanner.to_table()
if len(arrow_table) < 1:
return None
return to_requested_schema(projected_schema, file_project_schema, arrow_table)
def _read_all_delete_files(fs: FileSystem, tasks: Iterable[FileScanTask]) -> Dict[str, List[ChunkedArray]]:
deletes_per_file: Dict[str, List[ChunkedArray]] = {}
unique_deletes = set(itertools.chain.from_iterable([task.delete_files for task in tasks]))
if len(unique_deletes) > 0:
executor = ExecutorFactory.get_or_create()
deletes_per_files: Iterator[Dict[str, ChunkedArray]] = executor.map(
lambda args: _read_deletes(*args), [(fs, delete) for delete in unique_deletes]
)
for delete in deletes_per_files:
for file, arr in delete.items():
if file in deletes_per_file:
deletes_per_file[file].append(arr)
else:
deletes_per_file[file] = [arr]
return deletes_per_file
def project_table(
tasks: Iterable[FileScanTask],
table_metadata: TableMetadata,
io: FileIO,
row_filter: BooleanExpression,
projected_schema: Schema,
case_sensitive: bool = True,
limit: Optional[int] = None,
) -> pa.Table:
"""Resolve the right columns based on the identifier.
Args:
tasks (Iterable[FileScanTask]): A URI or a path to a local file.
table_metadata (TableMetadata): The table metadata of the table that's being queried
io (FileIO): A FileIO to open streams to the object store
row_filter (BooleanExpression): The expression for filtering rows.
projected_schema (Schema): The output schema.
case_sensitive (bool): Case sensitivity when looking up column names.
limit (Optional[int]): Limit the number of records.
Raises:
ResolveError: When an incompatible query is done.
"""
scheme, netloc, _ = PyArrowFileIO.parse_location(table_metadata.location)
if isinstance(io, PyArrowFileIO):
fs = io.fs_by_scheme(scheme, netloc)
else:
try:
from pyiceberg.io.fsspec import FsspecFileIO
if isinstance(io, FsspecFileIO):
from pyarrow.fs import PyFileSystem
fs = PyFileSystem(FSSpecHandler(io.get_fs(scheme)))
else:
raise ValueError(f"Expected PyArrowFileIO or FsspecFileIO, got: {io}")
except ModuleNotFoundError as e:
# When FsSpec is not installed
raise ValueError(f"Expected PyArrowFileIO or FsspecFileIO, got: {io}") from e
bound_row_filter = bind(table_metadata.schema(), row_filter, case_sensitive=case_sensitive)
projected_field_ids = {
id for id in projected_schema.field_ids if not isinstance(projected_schema.find_type(id), (MapType, ListType))
}.union(extract_field_ids(bound_row_filter))
deletes_per_file = _read_all_delete_files(fs, tasks)
executor = ExecutorFactory.get_or_create()
futures = [
executor.submit(
_task_to_table,
fs,
task,
bound_row_filter,
projected_schema,
projected_field_ids,
deletes_per_file.get(task.file.file_path),
case_sensitive,
limit,
table_metadata.name_mapping(),
)
for task in tasks
]
total_row_count = 0
# for consistent ordering, we need to maintain future order
futures_index = {f: i for i, f in enumerate(futures)}
completed_futures: SortedList[Future[pa.Table]] = SortedList(iterable=[], key=lambda f: futures_index[f])
for future in concurrent.futures.as_completed(futures):
completed_futures.add(future)
if table_result := future.result():
total_row_count += len(table_result)
# stop early if limit is satisfied
if limit is not None and total_row_count >= limit:
break
# by now, we've either completed all tasks or satisfied the limit
if limit is not None:
_ = [f.cancel() for f in futures if not f.done()]
tables = [f.result() for f in completed_futures if f.result()]
if len(tables) < 1:
return pa.Table.from_batches([], schema=schema_to_pyarrow(projected_schema, include_field_ids=False))
result = pa.concat_tables(tables)
if limit is not None:
return result.slice(0, limit)
return result
def to_requested_schema(requested_schema: Schema, file_schema: Schema, table: pa.Table) -> pa.Table:
struct_array = visit_with_partner(requested_schema, table, ArrowProjectionVisitor(file_schema), ArrowAccessor(file_schema))
arrays = []
fields = []
for pos, field in enumerate(requested_schema.fields):
array = struct_array.field(pos)
arrays.append(array)
fields.append(pa.field(field.name, array.type, field.optional))
return pa.Table.from_arrays(arrays, schema=pa.schema(fields))
class ArrowProjectionVisitor(SchemaWithPartnerVisitor[pa.Array, Optional[pa.Array]]):
file_schema: Schema
def __init__(self, file_schema: Schema):
self.file_schema = file_schema
def _cast_if_needed(self, field: NestedField, values: pa.Array) -> pa.Array:
file_field = self.file_schema.find_field(field.field_id)
if field.field_type.is_primitive and field.field_type != file_field.field_type:
return values.cast(schema_to_pyarrow(promote(file_field.field_type, field.field_type), include_field_ids=False))
return values
def _construct_field(self, field: NestedField, arrow_type: pa.DataType) -> pa.Field:
return pa.field(
name=field.name,
type=arrow_type,
nullable=field.optional,
metadata={DOC: field.doc} if field.doc is not None else None,
)
def schema(self, schema: Schema, schema_partner: Optional[pa.Array], struct_result: Optional[pa.Array]) -> Optional[pa.Array]:
return struct_result
def struct(
self, struct: StructType, struct_array: Optional[pa.Array], field_results: List[Optional[pa.Array]]
) -> Optional[pa.Array]:
if struct_array is None:
return None
field_arrays: List[pa.Array] = []
fields: List[pa.Field] = []
for field, field_array in zip(struct.fields, field_results):
if field_array is not None:
array = self._cast_if_needed(field, field_array)
field_arrays.append(array)
fields.append(self._construct_field(field, array.type))
elif field.optional:
arrow_type = schema_to_pyarrow(field.field_type, include_field_ids=False)
field_arrays.append(pa.nulls(len(struct_array), type=arrow_type))
fields.append(self._construct_field(field, arrow_type))
else:
raise ResolveError(f"Field is required, and could not be found in the file: {field}")
return pa.StructArray.from_arrays(arrays=field_arrays, fields=pa.struct(fields))
def field(self, field: NestedField, _: Optional[pa.Array], field_array: Optional[pa.Array]) -> Optional[pa.Array]:
return field_array
def list(self, list_type: ListType, list_array: Optional[pa.Array], value_array: Optional[pa.Array]) -> Optional[pa.Array]:
if isinstance(list_array, pa.ListArray) and value_array is not None:
if isinstance(value_array, pa.StructArray):
# This can be removed once this has been fixed:
# https://github.com/apache/arrow/issues/38809
list_array = pa.ListArray.from_arrays(list_array.offsets, value_array)
arrow_field = pa.list_(self._construct_field(list_type.element_field, value_array.type))
return list_array.cast(arrow_field)
else:
return None
def map(
self, map_type: MapType, map_array: Optional[pa.Array], key_result: Optional[pa.Array], value_result: Optional[pa.Array]
) -> Optional[pa.Array]:
if isinstance(map_array, pa.MapArray) and key_result is not None and value_result is not None:
arrow_field = pa.map_(
self._construct_field(map_type.key_field, key_result.type),
self._construct_field(map_type.value_field, value_result.type),
)
if isinstance(value_result, pa.StructArray):
# Arrow does not allow reordering of fields, therefore we have to copy the array :(
return pa.MapArray.from_arrays(map_array.offsets, key_result, value_result, arrow_field)
else:
return map_array.cast(arrow_field)
else:
return None
def primitive(self, _: PrimitiveType, array: Optional[pa.Array]) -> Optional[pa.Array]:
return array
class ArrowAccessor(PartnerAccessor[pa.Array]):
file_schema: Schema
def __init__(self, file_schema: Schema):
self.file_schema = file_schema
def schema_partner(self, partner: Optional[pa.Array]) -> Optional[pa.Array]:
return partner
def field_partner(self, partner_struct: Optional[pa.Array], field_id: int, _: str) -> Optional[pa.Array]:
if partner_struct:
# use the field name from the file schema
try:
name = self.file_schema.find_field(field_id).name
except ValueError:
return None
if isinstance(partner_struct, pa.StructArray):
return partner_struct.field(name)
elif isinstance(partner_struct, pa.Table):
return partner_struct.column(name).combine_chunks()
return None
def list_element_partner(self, partner_list: Optional[pa.Array]) -> Optional[pa.Array]:
return partner_list.values if isinstance(partner_list, pa.ListArray) else None
def map_key_partner(self, partner_map: Optional[pa.Array]) -> Optional[pa.Array]:
return partner_map.keys if isinstance(partner_map, pa.MapArray) else None
def map_value_partner(self, partner_map: Optional[pa.Array]) -> Optional[pa.Array]:
return partner_map.items if isinstance(partner_map, pa.MapArray) else None
def _primitive_to_physical(iceberg_type: PrimitiveType) -> str:
return visit(iceberg_type, _PRIMITIVE_TO_PHYSICAL_TYPE_VISITOR)
class PrimitiveToPhysicalType(SchemaVisitorPerPrimitiveType[str]):
def schema(self, schema: Schema, struct_result: str) -> str:
raise ValueError(f"Expected primitive-type, got: {schema}")
def struct(self, struct: StructType, field_results: List[str]) -> str:
raise ValueError(f"Expected primitive-type, got: {struct}")
def field(self, field: NestedField, field_result: str) -> str:
raise ValueError(f"Expected primitive-type, got: {field}")
def list(self, list_type: ListType, element_result: str) -> str:
raise ValueError(f"Expected primitive-type, got: {list_type}")
def map(self, map_type: MapType, key_result: str, value_result: str) -> str:
raise ValueError(f"Expected primitive-type, got: {map_type}")
def visit_fixed(self, fixed_type: FixedType) -> str:
return "FIXED_LEN_BYTE_ARRAY"
def visit_decimal(self, decimal_type: DecimalType) -> str:
return "FIXED_LEN_BYTE_ARRAY"
def visit_boolean(self, boolean_type: BooleanType) -> str:
return "BOOLEAN"
def visit_integer(self, integer_type: IntegerType) -> str:
return "INT32"
def visit_long(self, long_type: LongType) -> str:
return "INT64"
def visit_float(self, float_type: FloatType) -> str:
return "FLOAT"
def visit_double(self, double_type: DoubleType) -> str:
return "DOUBLE"
def visit_date(self, date_type: DateType) -> str:
return "INT32"
def visit_time(self, time_type: TimeType) -> str:
return "INT64"
def visit_timestamp(self, timestamp_type: TimestampType) -> str:
return "INT64"
def visit_timestamptz(self, timestamptz_type: TimestamptzType) -> str:
return "INT64"
def visit_string(self, string_type: StringType) -> str:
return "BYTE_ARRAY"
def visit_uuid(self, uuid_type: UUIDType) -> str:
return "FIXED_LEN_BYTE_ARRAY"
def visit_binary(self, binary_type: BinaryType) -> str:
return "BYTE_ARRAY"
_PRIMITIVE_TO_PHYSICAL_TYPE_VISITOR = PrimitiveToPhysicalType()
class StatsAggregator:
current_min: Any
current_max: Any
trunc_length: Optional[int]
def __init__(self, iceberg_type: PrimitiveType, physical_type_string: str, trunc_length: Optional[int] = None) -> None:
self.current_min = None
self.current_max = None
self.trunc_length = trunc_length
expected_physical_type = _primitive_to_physical(iceberg_type)
if expected_physical_type != physical_type_string:
raise ValueError(
f"Unexpected physical type {physical_type_string} for {iceberg_type}, expected {expected_physical_type}"
)
self.primitive_type = iceberg_type
def serialize(self, value: Any) -> bytes:
return to_bytes(self.primitive_type, value)
def update_min(self, val: Optional[Any]) -> None:
if self.current_min is None:
self.current_min = val
elif val is not None:
self.current_min = min(val, self.current_min)
def update_max(self, val: Optional[Any]) -> None:
if self.current_max is None:
self.current_max = val
elif val is not None:
self.current_max = max(val, self.current_max)
def min_as_bytes(self) -> Optional[bytes]:
if self.current_min is None:
return None
return self.serialize(
self.current_min
if self.trunc_length is None
else TruncateTransform(width=self.trunc_length).transform(self.primitive_type)(self.current_min)
)
def max_as_bytes(self) -> Optional[bytes]:
if self.current_max is None:
return None
if self.primitive_type == StringType():
if not isinstance(self.current_max, str):
raise ValueError("Expected the current_max to be a string")
s_result = truncate_upper_bound_text_string(self.current_max, self.trunc_length)
return self.serialize(s_result) if s_result is not None else None
elif self.primitive_type == BinaryType():
if not isinstance(self.current_max, bytes):
raise ValueError("Expected the current_max to be bytes")
b_result = truncate_upper_bound_binary_string(self.current_max, self.trunc_length)
return self.serialize(b_result) if b_result is not None else None
else:
if self.trunc_length is not None:
raise ValueError(f"{self.primitive_type} cannot be truncated")
return self.serialize(self.current_max)
DEFAULT_TRUNCATION_LENGTH = 16
TRUNCATION_EXPR = r"^truncate\((\d+)\)$"
class MetricModeTypes(Enum):
TRUNCATE = "truncate"
NONE = "none"
COUNTS = "counts"
FULL = "full"
@dataclass(frozen=True)
class MetricsMode(Singleton):
type: MetricModeTypes
length: Optional[int] = None
def match_metrics_mode(mode: str) -> MetricsMode:
sanitized_mode = mode.strip().lower()
if sanitized_mode.startswith("truncate"):
m = re.match(TRUNCATION_EXPR, sanitized_mode)
if m:
length = int(m[1])
if length < 1:
raise ValueError("Truncation length must be larger than 0")
return MetricsMode(MetricModeTypes.TRUNCATE, int(m[1]))
else:
raise ValueError(f"Malformed truncate: {mode}")
elif sanitized_mode == "none":
return MetricsMode(MetricModeTypes.NONE)
elif sanitized_mode == "counts":
return MetricsMode(MetricModeTypes.COUNTS)
elif sanitized_mode == "full":
return MetricsMode(MetricModeTypes.FULL)
else:
raise ValueError(f"Unsupported metrics mode: {mode}")
@dataclass(frozen=True)
class StatisticsCollector:
field_id: int
iceberg_type: PrimitiveType
mode: MetricsMode
column_name: str
class PyArrowStatisticsCollector(PreOrderSchemaVisitor[List[StatisticsCollector]]):
_field_id: int = 0
_schema: Schema
_properties: Dict[str, str]
_default_mode: str
def __init__(self, schema: Schema, properties: Dict[str, str]):
self._schema = schema
self._properties = properties
self._default_mode = self._properties.get(
TableProperties.DEFAULT_WRITE_METRICS_MODE, TableProperties.DEFAULT_WRITE_METRICS_MODE_DEFAULT
)
def schema(self, schema: Schema, struct_result: Callable[[], List[StatisticsCollector]]) -> List[StatisticsCollector]:
return struct_result()
def struct(
self, struct: StructType, field_results: List[Callable[[], List[StatisticsCollector]]]
) -> List[StatisticsCollector]:
return list(itertools.chain(*[result() for result in field_results]))
def field(self, field: NestedField, field_result: Callable[[], List[StatisticsCollector]]) -> List[StatisticsCollector]:
self._field_id = field.field_id
return field_result()
def list(self, list_type: ListType, element_result: Callable[[], List[StatisticsCollector]]) -> List[StatisticsCollector]:
self._field_id = list_type.element_id
return element_result()
def map(
self,
map_type: MapType,
key_result: Callable[[], List[StatisticsCollector]],
value_result: Callable[[], List[StatisticsCollector]],
) -> List[StatisticsCollector]:
self._field_id = map_type.key_id
k = key_result()
self._field_id = map_type.value_id
v = value_result()
return k + v
def primitive(self, primitive: PrimitiveType) -> List[StatisticsCollector]:
column_name = self._schema.find_column_name(self._field_id)
if column_name is None:
return []
metrics_mode = match_metrics_mode(self._default_mode)
col_mode = self._properties.get(f"{TableProperties.METRICS_MODE_COLUMN_CONF_PREFIX}.{column_name}")
if col_mode:
metrics_mode = match_metrics_mode(col_mode)
if (
not (isinstance(primitive, StringType) or isinstance(primitive, BinaryType))
and metrics_mode.type == MetricModeTypes.TRUNCATE
):
metrics_mode = MetricsMode(MetricModeTypes.FULL)
is_nested = column_name.find(".") >= 0
if is_nested and metrics_mode.type in [MetricModeTypes.TRUNCATE, MetricModeTypes.FULL]:
metrics_mode = MetricsMode(MetricModeTypes.COUNTS)
return [StatisticsCollector(field_id=self._field_id, iceberg_type=primitive, mode=metrics_mode, column_name=column_name)]
def compute_statistics_plan(
schema: Schema,
table_properties: Dict[str, str],
) -> Dict[int, StatisticsCollector]:
"""
Compute the statistics plan for all columns.
The resulting list is assumed to have the same length and same order as the columns in the pyarrow table.
This allows the list to map from the column index to the Iceberg column ID.
For each element, the desired metrics collection that was provided by the user in the configuration
is computed and then adjusted according to the data type of the column. For nested columns the minimum
and maximum values are not computed. And truncation is only applied to text of binary strings.
Args:
table_properties (from pyiceberg.table.metadata.TableMetadata): The Iceberg table metadata properties.
They are required to compute the mapping of column position to iceberg schema type id. It's also
used to set the mode for column metrics collection
"""
stats_cols = pre_order_visit(schema, PyArrowStatisticsCollector(schema, table_properties))
result: Dict[int, StatisticsCollector] = {}
for stats_col in stats_cols:
result[stats_col.field_id] = stats_col
return result
@dataclass(frozen=True)
class ID2ParquetPath:
field_id: int
parquet_path: str
class ID2ParquetPathVisitor(PreOrderSchemaVisitor[List[ID2ParquetPath]]):
_field_id: int = 0
_path: List[str]
def __init__(self) -> None:
self._path = []
def schema(self, schema: Schema, struct_result: Callable[[], List[ID2ParquetPath]]) -> List[ID2ParquetPath]:
return struct_result()
def struct(self, struct: StructType, field_results: List[Callable[[], List[ID2ParquetPath]]]) -> List[ID2ParquetPath]:
return list(itertools.chain(*[result() for result in field_results]))
def field(self, field: NestedField, field_result: Callable[[], List[ID2ParquetPath]]) -> List[ID2ParquetPath]:
self._field_id = field.field_id
self._path.append(field.name)
result = field_result()
self._path.pop()
return result
def list(self, list_type: ListType, element_result: Callable[[], List[ID2ParquetPath]]) -> List[ID2ParquetPath]:
self._field_id = list_type.element_id
self._path.append("list.element")
result = element_result()
self._path.pop()
return result
def map(
self,
map_type: MapType,
key_result: Callable[[], List[ID2ParquetPath]],
value_result: Callable[[], List[ID2ParquetPath]],
) -> List[ID2ParquetPath]:
self._field_id = map_type.key_id
self._path.append("key_value.key")
k = key_result()
self._path.pop()
self._field_id = map_type.value_id
self._path.append("key_value.value")
v = value_result()
self._path.pop()
return k + v
def primitive(self, primitive: PrimitiveType) -> List[ID2ParquetPath]:
return [ID2ParquetPath(field_id=self._field_id, parquet_path=".".join(self._path))]
def parquet_path_to_id_mapping(
schema: Schema,
) -> Dict[str, int]:
"""
Compute the mapping of parquet column path to Iceberg ID.
For each column, the parquet file metadata has a path_in_schema attribute that follows
a specific naming scheme for nested columnds. This function computes a mapping of
the full paths to the corresponding Iceberg IDs.
Args:
schema (pyiceberg.schema.Schema): The current table schema.
"""
result: Dict[str, int] = {}
for pair in pre_order_visit(schema, ID2ParquetPathVisitor()):
result[pair.parquet_path] = pair.field_id
return result
@dataclass(frozen=True)
class DataFileStatistics:
record_count: int
column_sizes: Dict[int, int]
value_counts: Dict[int, int]
null_value_counts: Dict[int, int]
nan_value_counts: Dict[int, int]
column_aggregates: Dict[int, StatsAggregator]
split_offsets: List[int]
def _partition_value(self, partition_field: PartitionField, schema: Schema) -> Any:
if partition_field.source_id not in self.column_aggregates:
return None
if not partition_field.transform.preserves_order:
raise ValueError(
f"Cannot infer partition value from parquet metadata for a non-linear Partition Field: {partition_field.name} with transform {partition_field.transform}"
)
lower_value = partition_record_value(
partition_field=partition_field,
value=self.column_aggregates[partition_field.source_id].current_min,
schema=schema,
)
upper_value = partition_record_value(
partition_field=partition_field,
value=self.column_aggregates[partition_field.source_id].current_max,
schema=schema,
)
if lower_value != upper_value:
raise ValueError(
f"Cannot infer partition value from parquet metadata as there are more than one partition values for Partition Field: {partition_field.name}. {lower_value=}, {upper_value=}"
)
return lower_value
def partition(self, partition_spec: PartitionSpec, schema: Schema) -> Record:
return Record(**{field.name: self._partition_value(field, schema) for field in partition_spec.fields})
def to_serialized_dict(self) -> Dict[str, Any]:
lower_bounds = {}
upper_bounds = {}
for k, agg in self.column_aggregates.items():
_min = agg.min_as_bytes()
if _min is not None:
lower_bounds[k] = _min
_max = agg.max_as_bytes()
if _max is not None:
upper_bounds[k] = _max
return {
"record_count": self.record_count,
"column_sizes": self.column_sizes,
"value_counts": self.value_counts,
"null_value_counts": self.null_value_counts,
"nan_value_counts": self.nan_value_counts,
"lower_bounds": lower_bounds,
"upper_bounds": upper_bounds,
"split_offsets": self.split_offsets,
}
def data_file_statistics_from_parquet_metadata(
parquet_metadata: pq.FileMetaData,
stats_columns: Dict[int, StatisticsCollector],
parquet_column_mapping: Dict[str, int],
) -> DataFileStatistics:
"""
Compute and return DataFileStatistics that includes the following.
- record_count
- column_sizes
- value_counts
- null_value_counts
- nan_value_counts
- column_aggregates
- split_offsets
Args:
parquet_metadata (pyarrow.parquet.FileMetaData): A pyarrow metadata object.
stats_columns (Dict[int, StatisticsCollector]): The statistics gathering plan. It is required to
set the mode for column metrics collection
parquet_column_mapping (Dict[str, int]): The mapping of the parquet file name to the field ID
"""
if parquet_metadata.num_columns != len(stats_columns):
raise ValueError(
f"Number of columns in statistics configuration ({len(stats_columns)}) is different from the number of columns in pyarrow table ({parquet_metadata.num_columns})"
)
if parquet_metadata.num_columns != len(parquet_column_mapping):
raise ValueError(
f"Number of columns in column mapping ({len(parquet_column_mapping)}) is different from the number of columns in pyarrow table ({parquet_metadata.num_columns})"
)
column_sizes: Dict[int, int] = {}
value_counts: Dict[int, int] = {}
split_offsets: List[int] = []
null_value_counts: Dict[int, int] = {}
nan_value_counts: Dict[int, int] = {}
col_aggs = {}
for r in range(parquet_metadata.num_row_groups):
# References:
# https://github.com/apache/iceberg/blob/fc381a81a1fdb8f51a0637ca27cd30673bd7aad3/parquet/src/main/java/org/apache/iceberg/parquet/ParquetUtil.java#L232
# https://github.com/apache/parquet-mr/blob/ac29db4611f86a07cc6877b416aa4b183e09b353/parquet-hadoop/src/main/java/org/apache/parquet/hadoop/metadata/ColumnChunkMetaData.java#L184
row_group = parquet_metadata.row_group(r)
data_offset = row_group.column(0).data_page_offset
dictionary_offset = row_group.column(0).dictionary_page_offset
if row_group.column(0).has_dictionary_page and dictionary_offset < data_offset:
split_offsets.append(dictionary_offset)
else:
split_offsets.append(data_offset)
invalidate_col: Set[int] = set()
for pos in range(parquet_metadata.num_columns):
column = row_group.column(pos)
field_id = parquet_column_mapping[column.path_in_schema]
stats_col = stats_columns[field_id]
column_sizes.setdefault(field_id, 0)
column_sizes[field_id] += column.total_compressed_size
if stats_col.mode == MetricsMode(MetricModeTypes.NONE):
continue
value_counts[field_id] = value_counts.get(field_id, 0) + column.num_values
if column.is_stats_set:
try:
statistics = column.statistics
if statistics.has_null_count:
null_value_counts[field_id] = null_value_counts.get(field_id, 0) + statistics.null_count
if stats_col.mode == MetricsMode(MetricModeTypes.COUNTS):
continue
if field_id not in col_aggs:
col_aggs[field_id] = StatsAggregator(
stats_col.iceberg_type, statistics.physical_type, stats_col.mode.length
)
col_aggs[field_id].update_min(statistics.min)
col_aggs[field_id].update_max(statistics.max)
except pyarrow.lib.ArrowNotImplementedError as e:
invalidate_col.add(field_id)
logger.warning(e)
else:
invalidate_col.add(field_id)
logger.warning("PyArrow statistics missing for column %d when writing file", pos)
split_offsets.sort()
for field_id in invalidate_col:
del col_aggs[field_id]
del null_value_counts[field_id]
return DataFileStatistics(
record_count=parquet_metadata.num_rows,
column_sizes=column_sizes,
value_counts=value_counts,
null_value_counts=null_value_counts,
nan_value_counts=nan_value_counts,
column_aggregates=col_aggs,
split_offsets=split_offsets,
)
def write_file(io: FileIO, table_metadata: TableMetadata, tasks: Iterator[WriteTask]) -> Iterator[DataFile]:
parquet_writer_kwargs = _get_parquet_writer_kwargs(table_metadata.properties)
row_group_size = PropertyUtil.property_as_int(
properties=table_metadata.properties,
property_name=TableProperties.PARQUET_ROW_GROUP_SIZE_BYTES,
default=TableProperties.PARQUET_ROW_GROUP_SIZE_BYTES_DEFAULT,
)
def write_parquet(task: WriteTask) -> DataFile:
table_schema = task.schema
arrow_table = pa.Table.from_batches(task.record_batches)
# if schema needs to be transformed, use the transformed schema and adjust the arrow table accordingly
# otherwise use the original schema
if (sanitized_schema := sanitize_column_names(table_schema)) != table_schema:
file_schema = sanitized_schema
arrow_table = to_requested_schema(requested_schema=file_schema, file_schema=table_schema, table=arrow_table)
else:
file_schema = table_schema
file_path = f'{table_metadata.location}/data/{task.generate_data_file_path("parquet")}'
fo = io.new_output(file_path)
with fo.create(overwrite=True) as fos:
with pq.ParquetWriter(fos, schema=file_schema.as_arrow(), **parquet_writer_kwargs) as writer:
writer.write(arrow_table, row_group_size=row_group_size)
statistics = data_file_statistics_from_parquet_metadata(
parquet_metadata=writer.writer.metadata,
stats_columns=compute_statistics_plan(file_schema, table_metadata.properties),
parquet_column_mapping=parquet_path_to_id_mapping(file_schema),
)
data_file = DataFile(
content=DataFileContent.DATA,
file_path=file_path,
file_format=FileFormat.PARQUET,
partition=task.partition_key.partition if task.partition_key else Record(),
file_size_in_bytes=len(fo),
# After this has been fixed:
# https://github.com/apache/iceberg-python/issues/271
# sort_order_id=task.sort_order_id,
sort_order_id=None,
# Just copy these from the table for now
spec_id=table_metadata.default_spec_id,
equality_ids=None,
key_metadata=None,
**statistics.to_serialized_dict(),
)
return data_file
executor = ExecutorFactory.get_or_create()
data_files = executor.map(write_parquet, tasks)
return iter(data_files)
def bin_pack_arrow_table(tbl: pa.Table, target_file_size: int) -> Iterator[List[pa.RecordBatch]]:
from pyiceberg.utils.bin_packing import PackingIterator
avg_row_size_bytes = tbl.nbytes / tbl.num_rows
target_rows_per_file = target_file_size // avg_row_size_bytes
batches = tbl.to_batches(max_chunksize=target_rows_per_file)
bin_packed_record_batches = PackingIterator(
items=batches,
target_weight=target_file_size,
lookback=len(batches), # ignore lookback
weight_func=lambda x: x.nbytes,
largest_bin_first=False,
)
return bin_packed_record_batches
def parquet_files_to_data_files(io: FileIO, table_metadata: TableMetadata, file_paths: Iterator[str]) -> Iterator[DataFile]:
for file_path in file_paths:
input_file = io.new_input(file_path)
with input_file.open() as input_stream:
parquet_metadata = pq.read_metadata(input_stream)
if visit_pyarrow(parquet_metadata.schema.to_arrow_schema(), _HasIds()):
raise NotImplementedError(
f"Cannot add file {file_path} because it has field IDs. `add_files` only supports addition of files without field_ids"
)
schema = table_metadata.schema()
statistics = data_file_statistics_from_parquet_metadata(
parquet_metadata=parquet_metadata,
stats_columns=compute_statistics_plan(schema, table_metadata.properties),
parquet_column_mapping=parquet_path_to_id_mapping(schema),
)
data_file = DataFile(
content=DataFileContent.DATA,
file_path=file_path,
file_format=FileFormat.PARQUET,
partition=statistics.partition(table_metadata.spec(), table_metadata.schema()),
file_size_in_bytes=len(input_file),
sort_order_id=None,
spec_id=table_metadata.default_spec_id,
equality_ids=None,
key_metadata=None,
**statistics.to_serialized_dict(),
)
yield data_file
ICEBERG_UNCOMPRESSED_CODEC = "uncompressed"
PYARROW_UNCOMPRESSED_CODEC = "none"
def _get_parquet_writer_kwargs(table_properties: Properties) -> Dict[str, Any]:
for key_pattern in [
TableProperties.PARQUET_ROW_GROUP_SIZE_BYTES,
TableProperties.PARQUET_PAGE_ROW_LIMIT,
TableProperties.PARQUET_BLOOM_FILTER_MAX_BYTES,
f"{TableProperties.PARQUET_BLOOM_FILTER_COLUMN_ENABLED_PREFIX}.*",
]:
if unsupported_keys := fnmatch.filter(table_properties, key_pattern):
raise NotImplementedError(f"Parquet writer option(s) {unsupported_keys} not implemented")
compression_codec = table_properties.get(TableProperties.PARQUET_COMPRESSION, TableProperties.PARQUET_COMPRESSION_DEFAULT)
compression_level = PropertyUtil.property_as_int(
properties=table_properties,
property_name=TableProperties.PARQUET_COMPRESSION_LEVEL,
default=TableProperties.PARQUET_COMPRESSION_LEVEL_DEFAULT,
)
if compression_codec == ICEBERG_UNCOMPRESSED_CODEC:
compression_codec = PYARROW_UNCOMPRESSED_CODEC
return {
"compression": compression_codec,
"compression_level": compression_level,
"data_page_size": PropertyUtil.property_as_int(
properties=table_properties,
property_name=TableProperties.PARQUET_PAGE_SIZE_BYTES,
default=TableProperties.PARQUET_PAGE_SIZE_BYTES_DEFAULT,
),
"dictionary_pagesize_limit": PropertyUtil.property_as_int(
properties=table_properties,
property_name=TableProperties.PARQUET_DICT_SIZE_BYTES,
default=TableProperties.PARQUET_DICT_SIZE_BYTES_DEFAULT,
),
"write_batch_size": PropertyUtil.property_as_int(
properties=table_properties,
property_name=TableProperties.PARQUET_PAGE_ROW_LIMIT,
default=TableProperties.PARQUET_PAGE_ROW_LIMIT_DEFAULT,
),
}
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