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pyarrow.py
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pyarrow.py
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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
import uuid
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, BoundIsNaN, BoundIsNull, BoundTerm, Not, Or
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 (
AWS_ACCESS_KEY_ID,
AWS_REGION,
AWS_SECRET_ACCESS_KEY,
AWS_SESSION_TOKEN,
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, PartitionFieldValue, PartitionKey, PartitionSpec, partition_record_value
from pyiceberg.schema import (
PartnerAccessor,
PreOrderSchemaVisitor,
Schema,
SchemaVisitorPerPrimitiveType,
SchemaWithPartnerVisitor,
_check_schema_compatible,
pre_order_visit,
promote,
prune_columns,
sanitize_column_names,
visit,
visit_with_partner,
)
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.config import Config
from pyiceberg.utils.datetime import millis_to_datetime
from pyiceberg.utils.deprecated import deprecated
from pyiceberg.utils.properties import get_first_property_value, property_as_int
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, WriteTask
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"
UTC_ALIASES = {"UTC", "+00:00", "Etc/UTC", "Z"}
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": get_first_property_value(self.properties, S3_ACCESS_KEY_ID, AWS_ACCESS_KEY_ID),
"secret_key": get_first_property_value(self.properties, S3_SECRET_ACCESS_KEY, AWS_SECRET_ACCESS_KEY),
"session_token": get_first_property_value(self.properties, S3_SESSION_TOKEN, AWS_SESSION_TOKEN),
"region": get_first_property_value(self.properties, S3_REGION, AWS_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.large_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.large_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[Any], 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[Any], 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
class _NullNaNUnmentionedTermsCollector(BoundBooleanExpressionVisitor[None]):
# BoundTerms which have either is_null or is_not_null appearing at least once in the boolean expr.
is_null_or_not_bound_terms: set[BoundTerm[Any]]
# The remaining BoundTerms appearing in the boolean expr.
null_unmentioned_bound_terms: set[BoundTerm[Any]]
# BoundTerms which have either is_nan or is_not_nan appearing at least once in the boolean expr.
is_nan_or_not_bound_terms: set[BoundTerm[Any]]
# The remaining BoundTerms appearing in the boolean expr.
nan_unmentioned_bound_terms: set[BoundTerm[Any]]
def __init__(self) -> None:
super().__init__()
self.is_null_or_not_bound_terms = set()
self.null_unmentioned_bound_terms = set()
self.is_nan_or_not_bound_terms = set()
self.nan_unmentioned_bound_terms = set()
def _handle_explicit_is_null_or_not(self, term: BoundTerm[Any]) -> None:
"""Handle the predicate case where either is_null or is_not_null is included."""
if term in self.null_unmentioned_bound_terms:
self.null_unmentioned_bound_terms.remove(term)
self.is_null_or_not_bound_terms.add(term)
def _handle_null_unmentioned(self, term: BoundTerm[Any]) -> None:
"""Handle the predicate case where neither is_null or is_not_null is included."""
if term not in self.is_null_or_not_bound_terms:
self.null_unmentioned_bound_terms.add(term)
def _handle_explicit_is_nan_or_not(self, term: BoundTerm[Any]) -> None:
"""Handle the predicate case where either is_nan or is_not_nan is included."""
if term in self.nan_unmentioned_bound_terms:
self.nan_unmentioned_bound_terms.remove(term)
self.is_nan_or_not_bound_terms.add(term)
def _handle_nan_unmentioned(self, term: BoundTerm[Any]) -> None:
"""Handle the predicate case where neither is_nan or is_not_nan is included."""
if term not in self.is_nan_or_not_bound_terms:
self.nan_unmentioned_bound_terms.add(term)
def visit_in(self, term: BoundTerm[Any], literals: Set[Any]) -> None:
self._handle_null_unmentioned(term)
self._handle_nan_unmentioned(term)
def visit_not_in(self, term: BoundTerm[Any], literals: Set[Any]) -> None:
self._handle_null_unmentioned(term)
self._handle_nan_unmentioned(term)
def visit_is_nan(self, term: BoundTerm[Any]) -> None:
self._handle_null_unmentioned(term)
self._handle_explicit_is_nan_or_not(term)
def visit_not_nan(self, term: BoundTerm[Any]) -> None:
self._handle_null_unmentioned(term)
self._handle_explicit_is_nan_or_not(term)
def visit_is_null(self, term: BoundTerm[Any]) -> None:
self._handle_explicit_is_null_or_not(term)
self._handle_nan_unmentioned(term)
def visit_not_null(self, term: BoundTerm[Any]) -> None:
self._handle_explicit_is_null_or_not(term)
self._handle_nan_unmentioned(term)
def visit_equal(self, term: BoundTerm[Any], literal: Literal[Any]) -> None:
self._handle_null_unmentioned(term)
self._handle_nan_unmentioned(term)
def visit_not_equal(self, term: BoundTerm[Any], literal: Literal[Any]) -> None:
self._handle_null_unmentioned(term)
self._handle_nan_unmentioned(term)
def visit_greater_than_or_equal(self, term: BoundTerm[Any], literal: Literal[Any]) -> None:
self._handle_null_unmentioned(term)
self._handle_nan_unmentioned(term)
def visit_greater_than(self, term: BoundTerm[Any], literal: Literal[Any]) -> None:
self._handle_null_unmentioned(term)
self._handle_nan_unmentioned(term)
def visit_less_than(self, term: BoundTerm[Any], literal: Literal[Any]) -> None:
self._handle_null_unmentioned(term)
self._handle_nan_unmentioned(term)
def visit_less_than_or_equal(self, term: BoundTerm[Any], literal: Literal[Any]) -> None:
self._handle_null_unmentioned(term)
self._handle_nan_unmentioned(term)
def visit_starts_with(self, term: BoundTerm[Any], literal: Literal[Any]) -> None:
self._handle_null_unmentioned(term)
self._handle_nan_unmentioned(term)
def visit_not_starts_with(self, term: BoundTerm[Any], literal: Literal[Any]) -> None:
self._handle_null_unmentioned(term)
self._handle_nan_unmentioned(term)
def visit_true(self) -> None:
return
def visit_false(self) -> None:
return
def visit_not(self, child_result: None) -> None:
return
def visit_and(self, left_result: None, right_result: None) -> None:
return
def visit_or(self, left_result: None, right_result: None) -> None:
return
def collect(
self,
expr: BooleanExpression,
) -> None:
"""Collect the bound references categorized by having at least one is_null or is_not_null in the expr and the remaining."""
boolean_expression_visit(expr, self)
def expression_to_pyarrow(expr: BooleanExpression) -> pc.Expression:
return boolean_expression_visit(expr, _ConvertToArrowExpression())
def _expression_to_complementary_pyarrow(expr: BooleanExpression) -> pc.Expression:
"""Complementary filter conversion function of expression_to_pyarrow.
Could not use expression_to_pyarrow(Not(expr)) to achieve this complementary effect because ~ in pyarrow.compute.Expression does not handle null.
"""
collector = _NullNaNUnmentionedTermsCollector()
collector.collect(expr)
# Convert the set of terms to a sorted list so that layout of the expression to build is deterministic.
null_unmentioned_bound_terms: List[BoundTerm[Any]] = sorted(
collector.null_unmentioned_bound_terms, key=lambda term: term.ref().field.name
)
nan_unmentioned_bound_terms: List[BoundTerm[Any]] = sorted(
collector.nan_unmentioned_bound_terms, key=lambda term: term.ref().field.name
)
preserve_expr: BooleanExpression = Not(expr)
for term in null_unmentioned_bound_terms:
preserve_expr = Or(preserve_expr, BoundIsNull(term=term))
for term in nan_unmentioned_bound_terms:
preserve_expr = Or(preserve_expr, BoundIsNaN(term=term))
return expression_to_pyarrow(preserve_expr)
@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], start_index: int, end_index: 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.subtract(np.setdiff1d(np.arange(start_index, end_index), all_chunks, assume_unique=False), start_index)
def pyarrow_to_schema(
schema: pa.Schema, name_mapping: Optional[NameMapping] = None, downcast_ns_timestamp_to_us: bool = False
) -> Schema:
has_ids = visit_pyarrow(schema, _HasIds())
if has_ids:
visitor = _ConvertToIceberg(downcast_ns_timestamp_to_us=downcast_ns_timestamp_to_us)
elif name_mapping is not None:
visitor = _ConvertToIceberg(name_mapping=name_mapping, downcast_ns_timestamp_to_us=downcast_ns_timestamp_to_us)
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, downcast_ns_timestamp_to_us: bool = False) -> Schema:
return visit_pyarrow(schema, _ConvertToIcebergWithoutIDs(downcast_ns_timestamp_to_us=downcast_ns_timestamp_to_us))
def _pyarrow_schema_ensure_large_types(schema: pa.Schema) -> pa.Schema:
return visit_pyarrow(schema, _ConvertToLargeTypes())
@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]