/
encode_arrow.go
598 lines (546 loc) · 20.8 KB
/
encode_arrow.go
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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.
package pqarrow
import (
"context"
"encoding/binary"
"errors"
"fmt"
"time"
"unsafe"
"github.com/apache/arrow/go/v11/arrow"
"github.com/apache/arrow/go/v11/arrow/array"
"github.com/apache/arrow/go/v11/arrow/bitutil"
"github.com/apache/arrow/go/v11/arrow/decimal128"
"github.com/apache/arrow/go/v11/arrow/memory"
"github.com/apache/arrow/go/v11/internal/utils"
"github.com/apache/arrow/go/v11/parquet"
"github.com/apache/arrow/go/v11/parquet/file"
"golang.org/x/xerrors"
)
// get the count of the number of leaf arrays for the type
func calcLeafCount(dt arrow.DataType) int {
switch dt.ID() {
case arrow.EXTENSION, arrow.SPARSE_UNION, arrow.DENSE_UNION:
panic("arrow type not implemented")
case arrow.LIST:
return calcLeafCount(dt.(*arrow.ListType).Elem())
case arrow.FIXED_SIZE_LIST:
return calcLeafCount(dt.(*arrow.FixedSizeListType).Elem())
case arrow.MAP:
return calcLeafCount(dt.(*arrow.MapType).ValueType())
case arrow.STRUCT:
nleaves := 0
for _, f := range dt.(*arrow.StructType).Fields() {
nleaves += calcLeafCount(f.Type)
}
return nleaves
default:
return 1
}
}
func nullableRoot(manifest *SchemaManifest, field *SchemaField) bool {
curField := field
nullable := field.Field.Nullable
for curField != nil {
nullable = curField.Field.Nullable
curField = manifest.GetParent(curField)
}
return nullable
}
// ArrowColumnWriter is a convenience object for easily writing arrow data to a specific
// set of columns in a parquet file. Since a single arrow array can itself be a nested type
// consisting of multiple columns of data, this will write to all of the appropriate leaves in
// the parquet file, allowing easy writing of nested columns.
type ArrowColumnWriter struct {
builders []*multipathLevelBuilder
leafCount int
colIdx int
rgw file.RowGroupWriter
}
// NewArrowColumnWriter returns a new writer using the chunked array to determine the number of leaf columns,
// and the provided schema manifest to determine the paths for writing the columns.
//
// Using an arrow column writer is a convenience to avoid having to process the arrow array yourself
// and determine the correct definition and repetition levels manually.
func NewArrowColumnWriter(data *arrow.Chunked, offset, size int64, manifest *SchemaManifest, rgw file.RowGroupWriter, col int) (ArrowColumnWriter, error) {
if data.Len() == 0 {
return ArrowColumnWriter{leafCount: calcLeafCount(data.DataType()), rgw: rgw}, nil
}
var (
absPos int64
chunkOffset int64
chunkIdx int
values int64
)
for idx, chnk := range data.Chunks() {
chunkIdx = idx
if absPos >= offset {
break
}
chunkLen := int64(chnk.Len())
if absPos+chunkLen > offset {
chunkOffset = offset - absPos
break
}
absPos += chunkLen
}
if absPos >= int64(data.Len()) {
return ArrowColumnWriter{}, xerrors.New("cannot write data at offset past end of chunked array")
}
leafCount := calcLeafCount(data.DataType())
isNullable := false
// row group writer hasn't been advanced yet so add 1 to the current
// which is the one this instance will start writing for
// colIdx := rgw.CurrentColumn() + 1
schemaField, err := manifest.GetColumnField(col)
if err != nil {
return ArrowColumnWriter{}, err
}
isNullable = nullableRoot(manifest, schemaField)
builders := make([]*multipathLevelBuilder, 0)
for values < size {
chunk := data.Chunk(chunkIdx)
available := int64(chunk.Len() - int(chunkOffset))
chunkWriteSize := utils.Min(size-values, available)
// the chunk offset will be 0 here except for possibly the first chunk
// because of the above advancing logic
arrToWrite := array.NewSlice(chunk, chunkOffset, chunkOffset+chunkWriteSize)
defer arrToWrite.Release()
if arrToWrite.Len() > 0 {
bldr, err := newMultipathLevelBuilder(arrToWrite, isNullable)
if err != nil {
return ArrowColumnWriter{}, nil
}
if leafCount != bldr.leafCount() {
return ArrowColumnWriter{}, fmt.Errorf("data type leaf_count != builder leafcount: %d - %d", leafCount, bldr.leafCount())
}
builders = append(builders, bldr)
}
if chunkWriteSize == available {
chunkOffset = 0
chunkIdx++
}
values += chunkWriteSize
}
return ArrowColumnWriter{builders: builders, leafCount: leafCount, rgw: rgw, colIdx: col}, nil
}
func (acw *ArrowColumnWriter) Write(ctx context.Context) error {
arrCtx := arrowCtxFromContext(ctx)
for leafIdx := 0; leafIdx < acw.leafCount; leafIdx++ {
var (
cw file.ColumnChunkWriter
err error
)
if acw.rgw.Buffered() {
cw, err = acw.rgw.(file.BufferedRowGroupWriter).Column(acw.colIdx + leafIdx)
} else {
cw, err = acw.rgw.(file.SerialRowGroupWriter).NextColumn()
}
if err != nil {
return err
}
for _, bldr := range acw.builders {
if leafIdx == 0 {
defer bldr.Release()
}
res, err := bldr.write(leafIdx, arrCtx)
if err != nil {
return err
}
defer res.Release()
if len(res.postListVisitedElems) != 1 {
return xerrors.New("lists with non-zero length null components are not supported")
}
rng := res.postListVisitedElems[0]
values := array.NewSlice(res.leafArr, rng.start, rng.end)
defer values.Release()
if err = WriteArrowToColumn(ctx, cw, values, res.defLevels, res.repLevels, res.leafIsNullable); err != nil {
return err
}
}
}
return nil
}
// WriteArrowToColumn writes apache arrow columnar data directly to a ColumnWriter.
// Returns non-nil error if the array data type is not compatible with the concrete
// writer type.
//
// leafArr is always a primitive (possibly dictionary encoded type).
// Leaf_field_nullable indicates whether the leaf array is considered nullable
// according to its schema in a Table or its parent array.
func WriteArrowToColumn(ctx context.Context, cw file.ColumnChunkWriter, leafArr arrow.Array, defLevels, repLevels []int16, leafFieldNullable bool) error {
// Leaf nulls are canonical when there is only a single null element after a list
// and it is at the leaf.
colLevelInfo := cw.LevelInfo()
singleNullable := (colLevelInfo.DefLevel == colLevelInfo.RepeatedAncestorDefLevel+1) && leafFieldNullable
maybeParentNulls := colLevelInfo.HasNullableValues() && !singleNullable
if maybeParentNulls && !cw.HasBitsBuffer() {
buf := memory.NewResizableBuffer(cw.Properties().Allocator())
buf.Resize(int(bitutil.BytesForBits(cw.Properties().WriteBatchSize())))
cw.SetBitsBuffer(buf)
}
if leafArr.DataType().ID() == arrow.DICTIONARY {
// TODO(mtopol): write arrow dictionary ARROW-7283
return errors.New("parquet/pqarrow: dictionary columns not yet implemented for WriteArrowToColumn")
}
return writeDenseArrow(arrowCtxFromContext(ctx), cw, leafArr, defLevels, repLevels, maybeParentNulls)
}
type binaryarr interface {
ValueOffsets() []int32
}
func writeDenseArrow(ctx *arrowWriteContext, cw file.ColumnChunkWriter, leafArr arrow.Array, defLevels, repLevels []int16, maybeParentNulls bool) (err error) {
noNulls := cw.Descr().SchemaNode().RepetitionType() == parquet.Repetitions.Required || leafArr.NullN() == 0
if ctx.dataBuffer == nil {
ctx.dataBuffer = memory.NewResizableBuffer(cw.Properties().Allocator())
}
switch wr := cw.(type) {
case *file.BooleanColumnChunkWriter:
if leafArr.DataType().ID() != arrow.BOOL {
return fmt.Errorf("type mismatch, column is %s, array is %s", cw.Type(), leafArr.DataType().ID())
}
// TODO(mtopol): optimize this so that we aren't converting from
// the bitmap -> []bool -> bitmap anymore
if leafArr.Len() == 0 {
wr.WriteBatch(nil, defLevels, repLevels)
break
}
ctx.dataBuffer.ResizeNoShrink(leafArr.Len())
buf := ctx.dataBuffer.Bytes()
data := *(*[]bool)(unsafe.Pointer(&buf))
for idx := range data {
data[idx] = leafArr.(*array.Boolean).Value(idx)
}
if !maybeParentNulls && noNulls {
wr.WriteBatch(data, defLevels, repLevels)
} else {
wr.WriteBatchSpaced(data, defLevels, repLevels, leafArr.NullBitmapBytes(), int64(leafArr.Data().Offset()))
}
case *file.Int32ColumnChunkWriter:
var data []int32
switch leafArr.DataType().ID() {
case arrow.INT32:
data = leafArr.(*array.Int32).Int32Values()
case arrow.DATE32, arrow.UINT32:
data = arrow.Int32Traits.CastFromBytes(leafArr.Data().Buffers()[1].Bytes())
data = data[leafArr.Data().Offset() : leafArr.Data().Offset()+leafArr.Len()]
case arrow.TIME32:
if leafArr.DataType().(*arrow.Time32Type).Unit != arrow.Second {
data = arrow.Int32Traits.CastFromBytes(leafArr.Data().Buffers()[1].Bytes())
data = data[leafArr.Data().Offset() : leafArr.Data().Offset()+leafArr.Len()]
} else { // coerce time32 if necessary by multiplying by 1000
ctx.dataBuffer.ResizeNoShrink(arrow.Int32Traits.BytesRequired(leafArr.Len()))
data = arrow.Int32Traits.CastFromBytes(ctx.dataBuffer.Bytes())
for idx, val := range leafArr.(*array.Time32).Time32Values() {
data[idx] = int32(val) * 1000
}
}
case arrow.NULL:
wr.WriteBatchSpaced(nil, defLevels, repLevels, leafArr.NullBitmapBytes(), 0)
return
default:
// simple integral cases, parquet physical storage is int32 or int64
// so we have to create a new array of int32's for anything smaller than
// 32-bits
ctx.dataBuffer.ResizeNoShrink(arrow.Int32Traits.BytesRequired(leafArr.Len()))
data = arrow.Int32Traits.CastFromBytes(ctx.dataBuffer.Bytes())
switch leafArr.DataType().ID() {
case arrow.UINT8:
for idx, val := range leafArr.(*array.Uint8).Uint8Values() {
data[idx] = int32(val)
}
case arrow.INT8:
for idx, val := range leafArr.(*array.Int8).Int8Values() {
data[idx] = int32(val)
}
case arrow.UINT16:
for idx, val := range leafArr.(*array.Uint16).Uint16Values() {
data[idx] = int32(val)
}
case arrow.INT16:
for idx, val := range leafArr.(*array.Int16).Int16Values() {
data[idx] = int32(val)
}
case arrow.DATE64:
for idx, val := range leafArr.(*array.Date64).Date64Values() {
data[idx] = int32(val / 86400000) // coerce date64 values
}
default:
return fmt.Errorf("type mismatch, column is int32 writer, arrow array is %s, and not a compatible type", leafArr.DataType().Name())
}
}
if !maybeParentNulls && noNulls {
wr.WriteBatch(data, defLevels, repLevels)
} else {
nulls := leafArr.NullBitmapBytes()
wr.WriteBatchSpaced(data, defLevels, repLevels, nulls, int64(leafArr.Data().Offset()))
}
case *file.Int64ColumnChunkWriter:
var data []int64
switch leafArr.DataType().ID() {
case arrow.TIMESTAMP:
tstype := leafArr.DataType().(*arrow.TimestampType)
if ctx.props.coerceTimestamps {
// user explicitly requested coercion to specific unit
if tstype.Unit == ctx.props.coerceTimestampUnit {
// no conversion necessary
data = arrow.Int64Traits.CastFromBytes(leafArr.Data().Buffers()[1].Bytes())
data = data[leafArr.Data().Offset() : leafArr.Data().Offset()+leafArr.Len()]
} else {
ctx.dataBuffer.ResizeNoShrink(arrow.Int64Traits.BytesRequired(leafArr.Len()))
data = arrow.Int64Traits.CastFromBytes(ctx.dataBuffer.Bytes())
if err := writeCoerceTimestamps(leafArr.(*array.Timestamp), &ctx.props, data); err != nil {
return err
}
}
} else if (cw.Properties().Version() == parquet.V1_0 || cw.Properties().Version() == parquet.V2_4) && tstype.Unit == arrow.Nanosecond {
// absent superceding user instructions, when writing a Parquet Version <=2.4 File,
// timestamps in nano seconds are coerced to microseconds
ctx.dataBuffer.ResizeNoShrink(arrow.Int64Traits.BytesRequired(leafArr.Len()))
data = arrow.Int64Traits.CastFromBytes(ctx.dataBuffer.Bytes())
p := NewArrowWriterProperties(WithCoerceTimestamps(arrow.Microsecond), WithTruncatedTimestamps(true))
if err := writeCoerceTimestamps(leafArr.(*array.Timestamp), &p, data); err != nil {
return err
}
} else if tstype.Unit == arrow.Second {
// absent superceding user instructions, timestamps in seconds are coerced
// to milliseconds
p := NewArrowWriterProperties(WithCoerceTimestamps(arrow.Millisecond))
ctx.dataBuffer.ResizeNoShrink(arrow.Int64Traits.BytesRequired(leafArr.Len()))
data = arrow.Int64Traits.CastFromBytes(ctx.dataBuffer.Bytes())
if err := writeCoerceTimestamps(leafArr.(*array.Timestamp), &p, data); err != nil {
return err
}
} else {
// no data conversion neccessary
data = arrow.Int64Traits.CastFromBytes(leafArr.Data().Buffers()[1].Bytes())
data = data[leafArr.Data().Offset() : leafArr.Data().Offset()+leafArr.Len()]
}
case arrow.UINT32:
ctx.dataBuffer.ResizeNoShrink(arrow.Int64Traits.BytesRequired(leafArr.Len()))
data = arrow.Int64Traits.CastFromBytes(ctx.dataBuffer.Bytes())
for idx, val := range leafArr.(*array.Uint32).Uint32Values() {
data[idx] = int64(val)
}
case arrow.INT64:
data = leafArr.(*array.Int64).Int64Values()
case arrow.UINT64, arrow.TIME64, arrow.DATE64:
data = arrow.Int64Traits.CastFromBytes(leafArr.Data().Buffers()[1].Bytes())
data = data[leafArr.Data().Offset() : leafArr.Data().Offset()+leafArr.Len()]
default:
return fmt.Errorf("unimplemented arrow type to write to int64 column: %s", leafArr.DataType().Name())
}
if !maybeParentNulls && noNulls {
wr.WriteBatch(data, defLevels, repLevels)
} else {
nulls := leafArr.NullBitmapBytes()
wr.WriteBatchSpaced(data, defLevels, repLevels, nulls, int64(leafArr.Data().Offset()))
}
case *file.Int96ColumnChunkWriter:
if leafArr.DataType().ID() != arrow.TIMESTAMP {
return xerrors.New("unsupported arrow type to write to Int96 column")
}
ctx.dataBuffer.ResizeNoShrink(parquet.Int96Traits.BytesRequired(leafArr.Len()))
data := parquet.Int96Traits.CastFromBytes(ctx.dataBuffer.Bytes())
input := leafArr.(*array.Timestamp).TimestampValues()
unit := leafArr.DataType().(*arrow.TimestampType).Unit
for idx, val := range input {
arrowTimestampToImpalaTimestamp(unit, int64(val), &data[idx])
}
if !maybeParentNulls && noNulls {
wr.WriteBatch(data, defLevels, repLevels)
} else {
nulls := leafArr.NullBitmapBytes()
wr.WriteBatchSpaced(data, defLevels, repLevels, nulls, int64(leafArr.Data().Offset()))
}
case *file.Float32ColumnChunkWriter:
if leafArr.DataType().ID() != arrow.FLOAT32 {
return xerrors.New("invalid column type to write to Float")
}
if !maybeParentNulls && noNulls {
wr.WriteBatch(leafArr.(*array.Float32).Float32Values(), defLevels, repLevels)
} else {
wr.WriteBatchSpaced(leafArr.(*array.Float32).Float32Values(), defLevels, repLevels, leafArr.NullBitmapBytes(), int64(leafArr.Data().Offset()))
}
case *file.Float64ColumnChunkWriter:
if leafArr.DataType().ID() != arrow.FLOAT64 {
return xerrors.New("invalid column type to write to Float")
}
if !maybeParentNulls && noNulls {
wr.WriteBatch(leafArr.(*array.Float64).Float64Values(), defLevels, repLevels)
} else {
wr.WriteBatchSpaced(leafArr.(*array.Float64).Float64Values(), defLevels, repLevels, leafArr.NullBitmapBytes(), int64(leafArr.Data().Offset()))
}
case *file.ByteArrayColumnChunkWriter:
if leafArr.DataType().ID() != arrow.STRING && leafArr.DataType().ID() != arrow.BINARY {
return xerrors.New("invalid column type to write to ByteArray")
}
var (
offsets = leafArr.(binaryarr).ValueOffsets()
buffer = leafArr.Data().Buffers()[2]
valueBuf []byte
)
if buffer == nil {
valueBuf = []byte{}
} else {
valueBuf = buffer.Bytes()
}
data := make([]parquet.ByteArray, leafArr.Len())
for i := range data {
data[i] = parquet.ByteArray(valueBuf[offsets[i]:offsets[i+1]])
}
if !maybeParentNulls && noNulls {
wr.WriteBatch(data, defLevels, repLevels)
} else {
wr.WriteBatchSpaced(data, defLevels, repLevels, leafArr.NullBitmapBytes(), int64(leafArr.Data().Offset()))
}
case *file.FixedLenByteArrayColumnChunkWriter:
switch dt := leafArr.DataType().(type) {
case *arrow.FixedSizeBinaryType:
data := make([]parquet.FixedLenByteArray, leafArr.Len())
for idx := range data {
data[idx] = leafArr.(*array.FixedSizeBinary).Value(idx)
}
if !maybeParentNulls && noNulls {
wr.WriteBatch(data, defLevels, repLevels)
} else {
wr.WriteBatchSpaced(data, defLevels, repLevels, leafArr.NullBitmapBytes(), int64(leafArr.Data().Offset()))
}
case *arrow.Decimal128Type:
// parquet decimal are stored with FixedLength values where the length is
// proportional to the precision. Arrow's Decimal are always stored with 16/32
// bytes. thus the internal FLBA must be adjusted by the offset calculation
offset := int(bitutil.BytesForBits(int64(dt.BitWidth()))) - int(DecimalSize(dt.Precision))
ctx.dataBuffer.ResizeNoShrink((leafArr.Len() - leafArr.NullN()) * dt.BitWidth())
scratch := ctx.dataBuffer.Bytes()
typeLen := wr.Descr().TypeLength()
fixDecimalEndianness := func(in decimal128.Num) parquet.FixedLenByteArray {
out := scratch[offset : offset+typeLen]
binary.BigEndian.PutUint64(scratch, uint64(in.HighBits()))
binary.BigEndian.PutUint64(scratch[arrow.Uint64SizeBytes:], in.LowBits())
scratch = scratch[2*arrow.Uint64SizeBytes:]
return out
}
data := make([]parquet.FixedLenByteArray, leafArr.Len())
arr := leafArr.(*array.Decimal128)
if leafArr.NullN() == 0 {
for idx := range data {
data[idx] = fixDecimalEndianness(arr.Value(idx))
}
wr.WriteBatch(data, defLevels, repLevels)
} else {
for idx := range data {
if arr.IsValid(idx) {
data[idx] = fixDecimalEndianness(arr.Value(idx))
}
}
wr.WriteBatchSpaced(data, defLevels, repLevels, arr.NullBitmapBytes(), int64(arr.Data().Offset()))
}
default:
return xerrors.New("unimplemented")
}
default:
return xerrors.New("unknown column writer physical type")
}
return
}
type coerceType int8
const (
coerceInvalid coerceType = iota
coerceDivide
coerceMultiply
)
type coercePair struct {
typ coerceType
factor int64
}
var factors = map[arrow.TimeUnit]map[arrow.TimeUnit]coercePair{
arrow.Second: {
arrow.Second: {coerceInvalid, 0},
arrow.Millisecond: {coerceMultiply, 1000},
arrow.Microsecond: {coerceMultiply, 1000000},
arrow.Nanosecond: {coerceMultiply, 1000000000},
},
arrow.Millisecond: {
arrow.Second: {coerceInvalid, 0},
arrow.Millisecond: {coerceMultiply, 1},
arrow.Microsecond: {coerceMultiply, 1000},
arrow.Nanosecond: {coerceMultiply, 1000000},
},
arrow.Microsecond: {
arrow.Second: {coerceInvalid, 0},
arrow.Millisecond: {coerceDivide, 1000},
arrow.Microsecond: {coerceMultiply, 1},
arrow.Nanosecond: {coerceMultiply, 1000},
},
arrow.Nanosecond: {
arrow.Second: {coerceInvalid, 0},
arrow.Millisecond: {coerceDivide, 1000000},
arrow.Microsecond: {coerceDivide, 1000},
arrow.Nanosecond: {coerceMultiply, 1},
},
}
func writeCoerceTimestamps(arr *array.Timestamp, props *ArrowWriterProperties, out []int64) error {
source := arr.DataType().(*arrow.TimestampType).Unit
target := props.coerceTimestampUnit
truncation := props.allowTruncatedTimestamps
vals := arr.TimestampValues()
multiply := func(factor int64) error {
for idx, val := range vals {
out[idx] = int64(val) * factor
}
return nil
}
divide := func(factor int64) error {
for idx, val := range vals {
if !truncation && arr.IsValid(idx) && (int64(val)%factor != 0) {
return fmt.Errorf("casting from %s to %s would lose data", source, target)
}
out[idx] = int64(val) / factor
}
return nil
}
coerce := factors[source][target]
switch coerce.typ {
case coerceMultiply:
return multiply(coerce.factor)
case coerceDivide:
return divide(coerce.factor)
default:
panic("invalid coercion")
}
}
const (
julianEpochOffsetDays int64 = 2440588
nanoSecondsPerDay = 24 * 60 * 60 * 1000 * 1000 * 1000
)
func arrowTimestampToImpalaTimestamp(unit arrow.TimeUnit, t int64, out *parquet.Int96) {
var d time.Duration
switch unit {
case arrow.Second:
d = time.Duration(t) * time.Second
case arrow.Microsecond:
d = time.Duration(t) * time.Microsecond
case arrow.Millisecond:
d = time.Duration(t) * time.Millisecond
case arrow.Nanosecond:
d = time.Duration(t) * time.Nanosecond
}
julianDays := (int64(d.Hours()) / 24) + julianEpochOffsetDays
lastDayNanos := t % (nanoSecondsPerDay)
binary.LittleEndian.PutUint64((*out)[:8], uint64(lastDayNanos))
binary.LittleEndian.PutUint32((*out)[8:], uint32(julianDays))
}