Source code for apache_beam.io.avroio

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"""``PTransforms`` for reading from and writing to Avro files.

Provides two read ``PTransform``s, ``ReadFromAvro`` and ``ReadAllFromAvro``,
that produces a ``PCollection`` of records.
Each record of this ``PCollection`` will contain a single record read from
an Avro file. Records that are of simple types will be mapped into
corresponding Python types. Records that are of Avro type 'RECORD' will be
mapped to Python dictionaries that comply with the schema contained in the
Avro file that contains those records. In this case, keys of each dictionary
will contain the corresponding field names and will be of type ``string``
while the values of the dictionary will be of the type defined in the
corresponding Avro schema.

For example, if schema of the Avro file is the following.
{"namespace": "example.avro","type": "record","name": "User","fields":
[{"name": "name", "type": "string"},
{"name": "favorite_number",  "type": ["int", "null"]},
{"name": "favorite_color", "type": ["string", "null"]}]}

Then records generated by read transforms will be dictionaries of the
following form.
{'name': 'Alyssa', 'favorite_number': 256, 'favorite_color': None}).

Additionally, this module provides a write ``PTransform`` ``WriteToAvro``
that can be used to write a given ``PCollection`` of Python objects to an
Avro file.
"""
# pytype: skip-file
import ctypes
import os
from functools import partial
from typing import Any
from typing import Callable
from typing import Dict
from typing import List
from typing import Union

import fastavro
from fastavro.read import block_reader
from fastavro.write import Writer

import apache_beam as beam
from apache_beam.io import filebasedsink
from apache_beam.io import filebasedsource
from apache_beam.io import iobase
from apache_beam.io.filesystem import CompressionTypes
from apache_beam.io.filesystems import FileSystems
from apache_beam.io.iobase import Read
from apache_beam.portability.api import schema_pb2
from apache_beam.transforms import PTransform
from apache_beam.typehints import schemas

__all__ = [
    'ReadFromAvro',
    'ReadAllFromAvro',
    'ReadAllFromAvroContinuously',
    'WriteToAvro'
]


[docs]class ReadFromAvro(PTransform): """A `PTransform` for reading records from avro files. Each record of the resulting PCollection will contain a single record read from a source. Records that are of simple types will be mapped to beam Rows with a single `record` field containing the records value. Records that are of Avro type ``RECORD`` will be mapped to Beam rows that comply with the schema contained in the Avro file that contains those records. """ def __init__( self, file_pattern=None, min_bundle_size=0, validate=True, use_fastavro=True, as_rows=False): """Initializes :class:`ReadFromAvro`. Uses source :class:`~apache_beam.io._AvroSource` to read a set of Avro files defined by a given file pattern. If ``/mypath/myavrofiles*`` is a file-pattern that points to a set of Avro files, a :class:`~apache_beam.pvalue.PCollection` for the records in these Avro files can be created in the following manner. .. testcode:: with beam.Pipeline() as p: records = p | 'Read' >> beam.io.ReadFromAvro('/mypath/myavrofiles*') .. NOTE: We're not actually interested in this error; but if we get here, it means that the way of calling this transform hasn't changed. .. testoutput:: :hide: Traceback (most recent call last): ... OSError: No files found based on the file pattern Each record of this :class:`~apache_beam.pvalue.PCollection` will contain a single record read from a source. Records that are of simple types will be mapped into corresponding Python types. Records that are of Avro type ``RECORD`` will be mapped to Python dictionaries that comply with the schema contained in the Avro file that contains those records. In this case, keys of each dictionary will contain the corresponding field names and will be of type :class:`str` while the values of the dictionary will be of the type defined in the corresponding Avro schema. For example, if schema of the Avro file is the following. :: { "namespace": "example.avro", "type": "record", "name": "User", "fields": [ {"name": "name", "type": "string"}, {"name": "favorite_number", "type": ["int", "null"]}, {"name": "favorite_color", "type": ["string", "null"]} ] } Then records generated by :class:`~apache_beam.io._AvroSource` will be dictionaries of the following form. :: {'name': 'Alyssa', 'favorite_number': 256, 'favorite_color': None}). Args: file_pattern (str): the file glob to read min_bundle_size (int): the minimum size in bytes, to be considered when splitting the input into bundles. validate (bool): flag to verify that the files exist during the pipeline creation time. use_fastavro (bool): This flag is left for API backwards compatibility and no longer has an effect. Do not use. as_rows (bool): Whether to return a schema'd PCollection of Beam rows. """ super().__init__() self._source = _FastAvroSource( file_pattern, min_bundle_size, validate=validate) if as_rows: path = FileSystems.match([file_pattern], [1])[0].metadata_list[0].path with FileSystems.open(path) as fin: avro_schema = fastavro.reader(fin).writer_schema beam_schema = avro_schema_to_beam_schema(avro_schema) self._post_process = avro_dict_to_beam_row(avro_schema, beam_schema) else: self._post_process = None
[docs] def expand(self, pvalue): records = pvalue.pipeline | Read(self._source) if self._post_process: return records | beam.Map(self._post_process) else: return records
[docs] def display_data(self): return {'source_dd': self._source}
[docs]class ReadAllFromAvro(PTransform): """A ``PTransform`` for reading ``PCollection`` of Avro files. Uses source '_AvroSource' to read a ``PCollection`` of Avro files or file patterns and produce a ``PCollection`` of Avro records. This implementation is only tested with batch pipeline. In streaming, reading may happen with delay due to the limitation in ReShuffle involved. """ DEFAULT_DESIRED_BUNDLE_SIZE = 64 * 1024 * 1024 # 64MB def __init__( self, min_bundle_size=0, desired_bundle_size=DEFAULT_DESIRED_BUNDLE_SIZE, use_fastavro=True, with_filename=False, label='ReadAllFiles'): """Initializes ``ReadAllFromAvro``. Args: min_bundle_size: the minimum size in bytes, to be considered when splitting the input into bundles. desired_bundle_size: the desired size in bytes, to be considered when splitting the input into bundles. use_fastavro (bool): This flag is left for API backwards compatibility and no longer has an effect. Do not use. with_filename: If True, returns a Key Value with the key being the file name and the value being the actual data. If False, it only returns the data. """ source_from_file = partial(_FastAvroSource, min_bundle_size=min_bundle_size) self._read_all_files = filebasedsource.ReadAllFiles( True, CompressionTypes.AUTO, desired_bundle_size, min_bundle_size, source_from_file, with_filename) self.label = label
[docs] def expand(self, pvalue): return pvalue | self.label >> self._read_all_files
[docs]class ReadAllFromAvroContinuously(ReadAllFromAvro): """A ``PTransform`` for reading avro files in given file patterns. This PTransform acts as a Source and produces continuously a ``PCollection`` of Avro records. For more details, see ``ReadAllFromAvro`` for avro parsing settings; see ``apache_beam.io.fileio.MatchContinuously`` for watching settings. ReadAllFromAvroContinuously is experimental. No backwards-compatibility guarantees. Due to the limitation on Reshuffle, current implementation does not scale. """ _ARGS_FOR_MATCH = ( 'interval', 'has_deduplication', 'start_timestamp', 'stop_timestamp', 'match_updated_files', 'apply_windowing') _ARGS_FOR_READ = ( 'min_bundle_size', 'desired_bundle_size', 'use_fastavro', 'with_filename') def __init__(self, file_pattern, label='ReadAllFilesContinuously', **kwargs): """Initialize the ``ReadAllFromAvroContinuously`` transform. Accepts args for constructor args of both :class:`ReadAllFromAvro` and :class:`~apache_beam.io.fileio.MatchContinuously`. """ kwargs_for_match = { k: v for (k, v) in kwargs.items() if k in self._ARGS_FOR_MATCH } kwargs_for_read = { k: v for (k, v) in kwargs.items() if k in self._ARGS_FOR_READ } kwargs_additinal = { k: v for (k, v) in kwargs.items() if k not in self._ARGS_FOR_MATCH and k not in self._ARGS_FOR_READ } super().__init__(label=label, **kwargs_for_read, **kwargs_additinal) self._file_pattern = file_pattern self._kwargs_for_match = kwargs_for_match
[docs] def expand(self, pbegin): # Importing locally to prevent circular dependency issues. from apache_beam.io.fileio import MatchContinuously # TODO(BEAM-14497) always reshuffle once gbk always trigger works. return ( pbegin | MatchContinuously(self._file_pattern, **self._kwargs_for_match) | 'ReadAllFiles' >> self._read_all_files._disable_reshuffle())
class _AvroUtils(object): @staticmethod def advance_file_past_next_sync_marker(f, sync_marker): buf_size = 10000 data = f.read(buf_size) while data: pos = data.find(sync_marker) if pos >= 0: # Adjusting the current position to the ending position of the sync # marker. backtrack = len(data) - pos - len(sync_marker) f.seek(-1 * backtrack, os.SEEK_CUR) return True else: if f.tell() >= len(sync_marker): # Backtracking in case we partially read the sync marker during the # previous read. We only have to backtrack if there are at least # len(sync_marker) bytes before current position. We only have to # backtrack (len(sync_marker) - 1) bytes. f.seek(-1 * (len(sync_marker) - 1), os.SEEK_CUR) data = f.read(buf_size) class _FastAvroSource(filebasedsource.FileBasedSource): """A source for reading Avro files using the `fastavro` library. ``_FastAvroSource`` is implemented using the file-based source framework available in module 'filebasedsource'. Hence please refer to module 'filebasedsource' to fully understand how this source implements operations common to all file-based sources such as file-pattern expansion and splitting into bundles for parallel processing. TODO: remove ``_AvroSource`` in favor of using ``_FastAvroSource`` everywhere once it has been more widely tested """ def read_records(self, file_name, range_tracker): next_block_start = -1 def split_points_unclaimed(stop_position): if next_block_start >= stop_position: # Next block starts at or after the suggested stop position. Hence # there will not be split points to be claimed for the range ending at # suggested stop position. return 0 return iobase.RangeTracker.SPLIT_POINTS_UNKNOWN range_tracker.set_split_points_unclaimed_callback(split_points_unclaimed) start_offset = range_tracker.start_position() if start_offset is None: start_offset = 0 with self.open_file(file_name) as f: blocks = block_reader(f) sync_marker = blocks._header['sync'] # We have to start at current position if previous bundle ended at the # end of a sync marker. start_offset = max(0, start_offset - len(sync_marker)) f.seek(start_offset) _AvroUtils.advance_file_past_next_sync_marker(f, sync_marker) next_block_start = f.tell() while range_tracker.try_claim(next_block_start): block = next(blocks) next_block_start = block.offset + block.size for record in block: yield record _create_avro_source = _FastAvroSource
[docs]class WriteToAvro(beam.transforms.PTransform): """A ``PTransform`` for writing avro files. If the input has a schema, a corresponding avro schema will be automatically generated and used to write the output records.""" def __init__( self, file_path_prefix, schema=None, codec='deflate', file_name_suffix='', num_shards=0, shard_name_template=None, mime_type='application/x-avro', use_fastavro=True): """Initialize a WriteToAvro transform. Args: file_path_prefix: The file path to write to. The files written will begin with this prefix, followed by a shard identifier (see num_shards), and end in a common extension, if given by file_name_suffix. In most cases, only this argument is specified and num_shards, shard_name_template, and file_name_suffix use default values. schema: The schema to use (dict). codec: The codec to use for block-level compression. Any string supported by the Avro specification is accepted (for example 'null'). file_name_suffix: Suffix for the files written. num_shards: The number of files (shards) used for output. If not set, the service will decide on the optimal number of shards. Constraining the number of shards is likely to reduce the performance of a pipeline. Setting this value is not recommended unless you require a specific number of output files. shard_name_template: A template string containing placeholders for the shard number and shard count. When constructing a filename for a particular shard number, the upper-case letters 'S' and 'N' are replaced with the 0-padded shard number and shard count respectively. This argument can be '' in which case it behaves as if num_shards was set to 1 and only one file will be generated. The default pattern used is '-SSSSS-of-NNNNN' if None is passed as the shard_name_template. mime_type: The MIME type to use for the produced files, if the filesystem supports specifying MIME types. use_fastavro (bool): This flag is left for API backwards compatibility and no longer has an effect. Do not use. Returns: A WriteToAvro transform usable for writing. """ self._schema = schema self._sink_provider = lambda avro_schema: _create_avro_sink( file_path_prefix, avro_schema, codec, file_name_suffix, num_shards, shard_name_template, mime_type)
[docs] def expand(self, pcoll): if self._schema: avro_schema = self._schema records = pcoll else: try: beam_schema = schemas.schema_from_element_type(pcoll.element_type) except TypeError as exn: raise ValueError( "An explicit schema is required to write non-schema'd PCollections." ) from exn avro_schema = beam_schema_to_avro_schema(beam_schema) records = pcoll | beam.Map( beam_row_to_avro_dict(avro_schema, beam_schema)) self._sink = self._sink_provider(avro_schema) return records | beam.io.iobase.Write(self._sink)
[docs] def display_data(self): return {'sink_dd': self._sink}
def _create_avro_sink( file_path_prefix, schema, codec, file_name_suffix, num_shards, shard_name_template, mime_type): if "class 'avro.schema" in str(type(schema)): raise ValueError( 'You are using Avro IO with fastavro (default with Beam on ' 'Python 3), but supplying a schema parsed by avro-python3. ' 'Please change the schema to a dict.') return _FastAvroSink( file_path_prefix, schema, codec, file_name_suffix, num_shards, shard_name_template, mime_type) class _BaseAvroSink(filebasedsink.FileBasedSink): """A base for a sink for avro files. """ def __init__( self, file_path_prefix, schema, codec, file_name_suffix, num_shards, shard_name_template, mime_type): super().__init__( file_path_prefix, file_name_suffix=file_name_suffix, num_shards=num_shards, shard_name_template=shard_name_template, coder=None, mime_type=mime_type, # Compression happens at the block level using the supplied codec, and # not at the file level. compression_type=CompressionTypes.UNCOMPRESSED) self._schema = schema self._codec = codec def display_data(self): res = super().display_data() res['codec'] = str(self._codec) res['schema'] = str(self._schema) return res class _FastAvroSink(_BaseAvroSink): """A sink for avro files using FastAvro. """ def __init__( self, file_path_prefix, schema, codec, file_name_suffix, num_shards, shard_name_template, mime_type): super().__init__( file_path_prefix, schema, codec, file_name_suffix, num_shards, shard_name_template, mime_type) self.file_handle = None def open(self, temp_path): self.file_handle = super().open(temp_path) return Writer(self.file_handle, self._schema, self._codec) def write_record(self, writer, value): writer.write(value) def close(self, writer): writer.flush() self.file_handle.close() AVRO_PRIMITIVES_TO_BEAM_PRIMITIVES = { 'boolean': schema_pb2.BOOLEAN, 'int': schema_pb2.INT32, 'long': schema_pb2.INT64, 'float': schema_pb2.FLOAT, 'double': schema_pb2.DOUBLE, 'bytes': schema_pb2.BYTES, 'string': schema_pb2.STRING, } BEAM_PRIMITIVES_TO_AVRO_PRIMITIVES = { v: k for k, v in AVRO_PRIMITIVES_TO_BEAM_PRIMITIVES.items() } _AvroSchemaType = Union[str, List, Dict] def avro_union_type_to_beam_type(union_type: List) -> schema_pb2.FieldType: """convert an avro union type to a beam type if the union type is a nullable, and it is a nullable union of an avro primitive with a corresponding beam primitive then create a nullable beam field of the corresponding beam type, otherwise return an Any type. Args: union_type: the avro union type to convert. Returns: the beam type of the avro union. """ if len(union_type) == 2 and "null" in union_type: for avro_type in union_type: if avro_type in AVRO_PRIMITIVES_TO_BEAM_PRIMITIVES: return schema_pb2.FieldType( atomic_type=AVRO_PRIMITIVES_TO_BEAM_PRIMITIVES[avro_type], nullable=True) return schemas.typing_to_runner_api(Any) return schemas.typing_to_runner_api(Any) def avro_type_to_beam_type(avro_type: _AvroSchemaType) -> schema_pb2.FieldType: if isinstance(avro_type, str): return avro_type_to_beam_type({'type': avro_type}) elif isinstance(avro_type, list): # Union type return avro_union_type_to_beam_type(avro_type) type_name = avro_type['type'] if type_name in AVRO_PRIMITIVES_TO_BEAM_PRIMITIVES: return schema_pb2.FieldType( atomic_type=AVRO_PRIMITIVES_TO_BEAM_PRIMITIVES[type_name]) elif type_name in ('fixed', 'enum'): return schema_pb2.FieldType(atomic_type=schema_pb2.STRING) elif type_name == 'array': return schema_pb2.FieldType( array_type=schema_pb2.ArrayType( element_type=avro_type_to_beam_type(avro_type['items']))) elif type_name == 'map': return schema_pb2.FieldType( map_type=schema_pb2.MapType( key_type=schema_pb2.FieldType(atomic_type=schema_pb2.STRING), value_type=avro_type_to_beam_type(avro_type['values']))) elif type_name == 'record': return schema_pb2.FieldType( row_type=schema_pb2.RowType( schema=schema_pb2.Schema( fields=[ schemas.schema_field( f['name'], avro_type_to_beam_type(f['type'])) for f in avro_type['fields'] ]))) else: raise ValueError(f'Unable to convert {avro_type} to a Beam schema.') def avro_schema_to_beam_schema( avro_schema: _AvroSchemaType) -> schema_pb2.Schema: beam_type = avro_type_to_beam_type(avro_schema) if isinstance(avro_schema, dict) and avro_schema['type'] == 'record': return beam_type.row_type.schema else: return schema_pb2.Schema(fields=[schemas.schema_field('record', beam_type)]) def avro_dict_to_beam_row( avro_schema: _AvroSchemaType, beam_schema: schema_pb2.Schema) -> Callable[[Any], Any]: if isinstance(avro_schema, str): return avro_dict_to_beam_row({'type': avro_schema}) if avro_schema['type'] == 'record': to_row = avro_value_to_beam_value( schema_pb2.FieldType(row_type=schema_pb2.RowType(schema=beam_schema))) else: def to_row(record): return beam.Row(record=record) return beam.typehints.with_output_types( schemas.named_tuple_from_schema(beam_schema))( to_row) def avro_atomic_value_to_beam_atomic_value(avro_type: str, value): """convert an avro atomic value to a beam atomic value if the avro type is an int or long, convert the value into from signed to unsigned because VarInt.java expects the number to be unsigned when decoding the number. Args: avro_type: the avro type of the corresponding value. value: the avro atomic value. Returns: the converted beam atomic value. """ if value is None: return value elif avro_type == "int": return ctypes.c_uint32(value).value elif avro_type == "long": return ctypes.c_uint64(value).value else: return value def avro_value_to_beam_value( beam_type: schema_pb2.FieldType) -> Callable[[Any], Any]: type_info = beam_type.WhichOneof("type_info") if type_info == "atomic_type": avro_type = BEAM_PRIMITIVES_TO_AVRO_PRIMITIVES[beam_type.atomic_type] return lambda value: avro_atomic_value_to_beam_atomic_value( avro_type, value) elif type_info == "array_type": element_converter = avro_value_to_beam_value( beam_type.array_type.element_type) return lambda value: [element_converter(e) for e in value] elif type_info == "iterable_type": element_converter = avro_value_to_beam_value( beam_type.iterable_type.element_type) return lambda value: [element_converter(e) for e in value] elif type_info == "map_type": if beam_type.map_type.key_type.atomic_type != schema_pb2.STRING: raise TypeError( f'Only strings allowed as map keys when converting from AVRO, ' f'found {beam_type}') value_converter = avro_value_to_beam_value(beam_type.map_type.value_type) return lambda value: {k: value_converter(v) for (k, v) in value.items()} elif type_info == "row_type": converters = { field.name: avro_value_to_beam_value(field.type) for field in beam_type.row_type.schema.fields } return lambda value: beam.Row( ** {name: convert(value[name]) for (name, convert) in converters.items()}) elif type_info == "logical_type": return lambda value: value else: raise ValueError(f"Unrecognized type_info: {type_info!r}") def beam_schema_to_avro_schema( beam_schema: schema_pb2.Schema) -> _AvroSchemaType: return beam_type_to_avro_type( schema_pb2.FieldType(row_type=schema_pb2.RowType(schema=beam_schema))) def unnest_primitive_type(beam_type: schema_pb2.FieldType): """unnests beam types that map to avro primitives or unions. if mapping to a avro primitive or a union, don't nest the field type for complex types, like arrays, we need to nest the type. Example: { 'type': 'string' } -> 'string' { 'type': 'array', 'items': 'string' } -> { 'type': 'array', 'items': 'string' } Args: beam_type: the beam type to map to avro. Returns: the converted avro type with the primitive or union type unnested. """ avro_type = beam_type_to_avro_type(beam_type) return avro_type['type'] if beam_type.WhichOneof( "type_info") == "atomic_type" else avro_type def beam_type_to_avro_type(beam_type: schema_pb2.FieldType) -> _AvroSchemaType: type_info = beam_type.WhichOneof("type_info") if type_info == "atomic_type": avro_primitive = BEAM_PRIMITIVES_TO_AVRO_PRIMITIVES[beam_type.atomic_type] avro_type = [ avro_primitive, 'null' ] if beam_type.nullable else avro_primitive return {'type': avro_type} elif type_info == "array_type": return { 'type': 'array', 'items': unnest_primitive_type(beam_type.array_type.element_type) } elif type_info == "iterable_type": return { 'type': 'array', 'items': unnest_primitive_type(beam_type.iterable_type.element_type) } elif type_info == "map_type": if beam_type.map_type.key_type.atomic_type != schema_pb2.STRING: raise TypeError( f'Only strings allowed as map keys when converting to AVRO, ' f'found {beam_type}') return { 'type': 'map', 'values': unnest_primitive_type(beam_type.map_type.element_type) } elif type_info == "row_type": return { 'type': 'record', 'name': beam_type.row_type.schema.id, 'fields': [{ 'name': field.name, 'type': unnest_primitive_type(field.type) } for field in beam_type.row_type.schema.fields], } else: raise ValueError(f"Unconvertable type: {beam_type}") def beam_row_to_avro_dict( avro_schema: _AvroSchemaType, beam_schema: schema_pb2.Schema): if isinstance(avro_schema, str): return beam_row_to_avro_dict({'type': avro_schema}, beam_schema) if avro_schema['type'] == 'record': return beam_value_to_avro_value( schema_pb2.FieldType(row_type=schema_pb2.RowType(schema=beam_schema))) else: convert = beam_value_to_avro_value(beam_schema) return lambda row: convert(row[0]) def beam_atomic_value_to_avro_atomic_value(avro_type: str, value): """convert a beam atomic value to an avro atomic value since numeric values are converted to unsigned in avro_atomic_value_to_beam_atomic_value we need to convert back to a signed number. Args: avro_type: avro type of the corresponding value. value: the beam atomic value. Returns: the converted avro atomic value. """ if value is None: return value elif avro_type == "int": return ctypes.c_int32(value).value elif avro_type == "long": return ctypes.c_int64(value).value else: return value def beam_value_to_avro_value( beam_type: schema_pb2.FieldType) -> Callable[[Any], Any]: type_info = beam_type.WhichOneof("type_info") if type_info == "atomic_type": avro_type = BEAM_PRIMITIVES_TO_AVRO_PRIMITIVES[beam_type.atomic_type] return lambda value: beam_atomic_value_to_avro_atomic_value( avro_type, value) elif type_info == "array_type": element_converter = beam_value_to_avro_value( beam_type.array_type.element_type) return lambda value: [element_converter(e) for e in value] elif type_info == "iterable_type": element_converter = beam_value_to_avro_value( beam_type.iterable_type.element_type) return lambda value: [element_converter(e) for e in value] elif type_info == "map_type": if beam_type.map_type.key_type.atomic_type != schema_pb2.STRING: raise TypeError( f'Only strings allowed as map keys when converting from AVRO, ' f'found {beam_type}') value_converter = beam_value_to_avro_value(beam_type.map_type.value_type) return lambda value: {k: value_converter(v) for (k, v) in value.items()} elif type_info == "row_type": converters = { field.name: beam_value_to_avro_value(field.type) for field in beam_type.row_type.schema.fields } return lambda value: { name: convert(getattr(value, name)) for (name, convert) in converters.items() } elif type_info == "logical_type": return lambda value: value else: raise ValueError(f"Unrecognized type_info: {type_info!r}")