/
variable_length.go
249 lines (202 loc) · 6.42 KB
/
variable_length.go
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package examples_lib
import (
"fmt"
tiledb "github.com/TileDB-Inc/TileDB-Go"
"github.com/TileDB-Inc/TileDB-Go/bytesizes"
)
const rowsVariableLengthTileExtent = 4
const colsVariableLengthTileExtent = 4
func createVariableLengthArray(dir string) {
// Create a TileDB context.
ctx, err := tiledb.NewContext(nil)
checkError(err)
defer ctx.Free()
// The array will be 4x4 with dimensions "rows" and "cols", with domain [1,4].
domain, err := tiledb.NewDomain(ctx)
checkError(err)
defer domain.Free()
rowDim, err := tiledb.NewDimension(ctx, "rows", tiledb.TILEDB_INT32, []int32{1, 4}, int32(rowsVariableLengthTileExtent))
checkError(err)
defer rowDim.Free()
colDim, err := tiledb.NewDimension(ctx, "cols", tiledb.TILEDB_INT32, []int32{1, 4}, int32(colsVariableLengthTileExtent))
checkError(err)
defer colDim.Free()
err = domain.AddDimensions(rowDim, colDim)
checkError(err)
// The array will be dense.
schema, err := tiledb.NewArraySchema(ctx, tiledb.TILEDB_DENSE)
checkError(err)
defer schema.Free()
err = schema.SetDomain(domain)
checkError(err)
err = schema.SetCellOrder(tiledb.TILEDB_ROW_MAJOR)
checkError(err)
err = schema.SetTileOrder(tiledb.TILEDB_ROW_MAJOR)
checkError(err)
// Add two variable-length attributes "a1" and "a2", the first storing
// strings and the second storing a variable number of integers.
a1, err := tiledb.NewAttribute(ctx, "a1", tiledb.TILEDB_STRING_ASCII)
checkError(err)
defer a1.Free()
a2, err := tiledb.NewAttribute(ctx, "a2", tiledb.TILEDB_INT32)
checkError(err)
defer a2.Free()
err = a1.SetCellValNum(tiledb.TILEDB_VAR_NUM)
checkError(err)
err = a1.SetFillValue("null")
checkError(err)
err = schema.AddAttributes(a1)
checkError(err)
err = a2.SetCellValNum(tiledb.TILEDB_VAR_NUM)
checkError(err)
err = schema.AddAttributes(a2)
checkError(err)
// Create the (empty) array on disk.
array, err := tiledb.NewArray(ctx, dir)
checkError(err)
defer array.Free()
err = array.Create(schema)
checkError(err)
}
func writeVariableLengthArray(dir string) {
ctx, err := tiledb.NewContext(nil)
checkError(err)
defer ctx.Free()
// Prepare some data for the array
a1Data := []byte("a" + "bb" + "ccc" + "dd" + "eee" + "f" + "g" + "hhh" +
"i" + "jjj" + "kk" + "l" + "m" + "n" + "oo" + "p")
a1Off := []uint64{
0, 1, 3, 6, 8, 11, 12, 13, 16, 17, 20, 22, 23, 24, 25, 27}
a2Data := []int32{
1, 1, 2, 2, 3, 4, 5, 6, 6, 7, 7, 8, 8,
8, 9, 9, 10, 11, 12, 12, 13, 14, 14, 14, 15, 16}
a2ElOff := []uint64{
0, 2, 4, 5, 6, 7, 9, 11, 14, 16, 17, 18, 20, 21, 24, 25}
a2Off := make([]uint64, 16)
for i := range a2ElOff {
a2Off[i] = a2ElOff[i] * bytesizes.Int32
}
// Open the array for writing and create the query.
array, err := tiledb.NewArray(ctx, dir)
checkError(err)
defer array.Free()
err = array.Open(tiledb.TILEDB_WRITE)
checkError(err)
defer array.Close()
query, err := tiledb.NewQuery(ctx, array)
checkError(err)
defer query.Free()
err = query.SetLayout(tiledb.TILEDB_ROW_MAJOR)
checkError(err)
_, _, err = query.SetBufferVar("a1", a1Off, a1Data)
checkError(err)
_, _, err = query.SetBufferVar("a2", a2Off, a2Data)
checkError(err)
// Perform the write
err = query.Submit()
checkError(err)
err = query.Finalize()
checkError(err)
}
func printResultsVariableLength(
a1Off []uint64,
a1Data []byte,
a2Off []uint64,
a2Data []int32,
resultElMap map[string][3]uint64) {
// Get the string sizes
resultElA1Off := resultElMap["a1"][0]
var a1StrSizes []uint64
for i := 0; i < int(resultElA1Off)-1; i++ {
a1StrSizes = append(a1StrSizes, a1Off[i+1]-a1Off[i])
}
resultA1DataSize := resultElMap["a1"][1] *
bytesizes.Byte
a1StrSizes = append(a1StrSizes,
resultA1DataSize-a1Off[resultElA1Off-1])
// Get the strings
a1Str := make([][]byte, resultElA1Off)
for i := 0; i < int(resultElA1Off); i++ {
a1Str[i] = make([]byte, 0)
for j := 0; j < int(a1StrSizes[i]); j++ {
a1Str[i] = append(a1Str[i], a1Data[a1Off[i]])
}
}
// Get the element offsets
var a2ElOff []uint64
resultElA2Off := resultElMap["a2"][0]
for i := 0; i < int(resultElA2Off); i++ {
a2ElOff = append(a2ElOff, a2Off[i]/bytesizes.Int32)
}
// Get the number of elements per cell value
var a2CellEl []uint64
for i := 0; i < int(resultElA2Off)-1; i++ {
a2CellEl = append(a2CellEl, a2ElOff[i+1]-a2ElOff[i])
}
resultElA2Data := resultElMap["a2"][1]
a2CellEl = append(a2CellEl, resultElA2Data-a2ElOff[len(a2ElOff)-1])
// Print the results
for i := 0; i < int(resultElA1Off); i++ {
fmt.Printf("a1: %s, a2: ", string(a1Str[i]))
for j := 0; j < int(a2CellEl[i]); j++ {
fmt.Printf("%d", a2Data[a2ElOff[i]+uint64(j)])
}
fmt.Printf("\n")
}
}
func readVariableLengthArray(dir string) {
// Create TileDB context
ctx, err := tiledb.NewContext(nil)
checkError(err)
defer ctx.Free()
// Prepare the array for reading
array, err := tiledb.NewArray(ctx, dir)
checkError(err)
defer array.Free()
err = array.Open(tiledb.TILEDB_READ)
checkError(err)
defer array.Close()
// Slice only rows 1, 2 and cols 2, 3, 4
subArray := []int32{1, 2, 2, 4}
// Prepare the query
query, err := tiledb.NewQuery(ctx, array)
checkError(err)
defer query.Free()
err = query.SetSubArray(subArray)
checkError(err)
bufferElements, err := query.EstimateBufferElements()
checkError(err)
a1Off := make([]uint64, bufferElements["a1"][0])
a1Data := make([]byte, bufferElements["a1"][1]*rowsVariableLengthTileExtent)
a2Off := make([]uint64, bufferElements["a2"][0])
a2Data := make([]int32, bufferElements["a2"][1]*colsVariableLengthTileExtent)
err = query.SetLayout(tiledb.TILEDB_ROW_MAJOR)
checkError(err)
_, _, err = query.SetBufferVar("a1", a1Off, a1Data)
checkError(err)
_, _, err = query.SetBufferVar("a2", a2Off, a2Data)
checkError(err)
sizeOff, sizeVal, err := query.EstResultSizeVar("a1")
checkError(err)
fmt.Printf("a1, Estimated offset size: %d, estimated query size in bytes: %d\n",
*sizeOff, *sizeVal)
sizeOff, sizeVal, err = query.EstResultSizeVar("a2")
checkError(err)
fmt.Printf("a2, Estimated offset size: %d, estimated query size in bytes: %d\n",
*sizeOff, *sizeVal)
// Submit the query and close the array.
err = query.Submit()
checkError(err)
elements, err := query.ResultBufferElements()
checkError(err)
printResultsVariableLength(a1Off, a1Data, a2Off, a2Data, elements)
err = query.Finalize()
checkError(err)
}
func RunVariableLengthArray() {
tmpDir := temp("variable_length_array")
defer cleanup(tmpDir)
createVariableLengthArray(tmpDir)
writeVariableLengthArray(tmpDir)
readVariableLengthArray(tmpDir)
}