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subarray_test.go
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package tiledb
import (
"testing"
"github.com/stretchr/testify/assert"
"github.com/stretchr/testify/require"
)
func TestSubarrayForDenseArray(t *testing.T) {
arrPath := createDenseIntegerGrid(t, 16)
arr := openArray(t, arrPath, TILEDB_READ)
t.Run("GetRange", func(t *testing.T) {
sa, err := arr.NewSubarray()
require.NoError(t, err)
rangeY, err := sa.GetRange(0, 0)
require.NoError(t, err)
checkRange[uint8](t, rangeY, 0, 15)
rangeX, err := sa.GetRange(1, 0)
require.NoError(t, err)
checkRange[uint8](t, rangeX, 0, 15)
})
t.Run("GetRangeFromName", func(t *testing.T) {
sa, err := arr.NewSubarray()
require.NoError(t, err)
rangeY, err := sa.GetRangeFromName("y", 0)
require.NoError(t, err)
checkRange[uint8](t, rangeY, 0, 15)
rangeX, err := sa.GetRangeFromName("x", 0)
require.NoError(t, err)
checkRange[uint8](t, rangeX, 0, 15)
})
t.Run("AddRange", func(t *testing.T) {
sa, err := arr.NewSubarray()
require.NoError(t, err)
require.NoError(t, sa.AddRange(0, MakeRange[uint8](0, 3)))
require.NoError(t, sa.AddRange(1, MakeRange[uint8](4, 7)))
rangeY, err := sa.GetRange(0, 0)
require.NoError(t, err)
checkRange[uint8](t, rangeY, 0, 3)
rangeX, err := sa.GetRange(1, 0)
require.NoError(t, err)
checkRange[uint8](t, rangeX, 4, 7)
})
t.Run("AddRangeChecks", func(t *testing.T) {
sa, err := arr.NewSubarray()
require.NoError(t, err)
err = sa.AddRange(0, MakeRange[uint32](0x04040404, 0x07070707))
require.Error(t, err)
assert.Contains(t, err.Error(), "mismatch, range: uint32 dimension: uint8")
})
t.Run("AddRangeByName", func(t *testing.T) {
sa, err := arr.NewSubarray()
require.NoError(t, err)
require.NoError(t, sa.AddRangeByName("y", MakeRange[uint8](0, 3)))
require.NoError(t, sa.AddRangeByName("x", MakeRange[uint8](4, 7)))
rangeY, err := sa.GetRangeFromName("y", 0)
require.NoError(t, err)
checkRange[uint8](t, rangeY, 0, 3)
rangeX, err := sa.GetRangeFromName("x", 0)
require.NoError(t, err)
checkRange[uint8](t, rangeX, 4, 7)
})
t.Run("AddRangeByNameChecks", func(t *testing.T) {
sa, err := arr.NewSubarray()
require.NoError(t, err)
err = sa.AddRangeByName("y", MakeRange[uint32](0x04040404, 0x07070707))
require.Error(t, err)
assert.Contains(t, err.Error(), "mismatch, range: uint32 dimension: uint8")
})
t.Run("AddRangeMixed", func(t *testing.T) {
sa, err := arr.NewSubarray()
require.NoError(t, err)
require.NoError(t, sa.AddRangeByName("y", MakeRange[uint8](0, 3)))
require.NoError(t, sa.AddRange(1, MakeRange[uint8](4, 7)))
rangeY, err := sa.GetRange(0, 0)
require.NoError(t, err)
checkRange[uint8](t, rangeY, 0, 3)
rangeX, err := sa.GetRangeFromName("x", 0)
require.NoError(t, err)
checkRange[uint8](t, rangeX, 4, 7)
})
}
func TestSubarrayForSparseArray(t *testing.T) {
arrPath := createSparse2dTable(t)
arr := openArray(t, arrPath, TILEDB_READ)
t.Run("GetRange", func(t *testing.T) {
sa, err := arr.NewSubarray()
require.NoError(t, err)
rangeS, err := sa.GetRange(0, 0)
require.NoError(t, err)
checkRange[string](t, rangeS, "", "")
rangeN, err := sa.GetRange(1, 0)
require.NoError(t, err)
checkRange[float32](t, rangeN, 0.0, 100.0)
})
t.Run("GetRangeFromName", func(t *testing.T) {
sa, err := arr.NewSubarray()
require.NoError(t, err)
rangeS, err := sa.GetRangeFromName("str", 0)
require.NoError(t, err)
checkRange[string](t, rangeS, "", "")
rangeN, err := sa.GetRangeFromName("num", 0)
require.NoError(t, err)
checkRange[float32](t, rangeN, 0.0, 100.0)
})
t.Run("AddRange", func(t *testing.T) {
sa, err := arr.NewSubarray()
require.NoError(t, err)
require.NoError(t, sa.AddRange(0, MakeRange("from", "to")))
require.NoError(t, sa.AddRange(1, MakeRange[float32](2.0, 4.0)))
rangeS, err := sa.GetRange(0, 0)
require.NoError(t, err)
checkRange[string](t, rangeS, "from", "to")
rangeN, err := sa.GetRange(1, 0)
require.NoError(t, err)
checkRange[float32](t, rangeN, 2.0, 4.0)
})
t.Run("AddRangeChecks", func(t *testing.T) {
sa, err := arr.NewSubarray()
require.NoError(t, err)
err = sa.AddRange(0, MakeRange[uint32](0x04040404, 0x07070707))
require.Error(t, err)
assert.Contains(t, err.Error(), "dimension is of variable size but range is not")
err = sa.AddRange(1, MakeRange[uint32](0x04040404, 0x07070707))
require.Error(t, err)
assert.Contains(t, err.Error(), "mismatch, range: uint32 dimension: float32")
})
t.Run("AddRangeByName", func(t *testing.T) {
sa, err := arr.NewSubarray()
require.NoError(t, err)
require.NoError(t, sa.AddRangeByName("str", MakeRange("from", "to")))
require.NoError(t, sa.AddRangeByName("num", MakeRange[float32](2.0, 4.0)))
rangeS, err := sa.GetRange(0, 0)
require.NoError(t, err)
checkRange[string](t, rangeS, "from", "to")
rangeN, err := sa.GetRange(1, 0)
require.NoError(t, err)
checkRange[float32](t, rangeN, 2.0, 4.0)
})
t.Run("AddRangeByNameChecks", func(t *testing.T) {
sa, err := arr.NewSubarray()
require.NoError(t, err)
err = sa.AddRangeByName("str", MakeRange[uint32](0x04040404, 0x07070707))
require.Error(t, err)
assert.Contains(t, err.Error(), "dimension is of variable size but range is not")
err = sa.AddRangeByName("num", MakeRange[uint32](0x04040404, 0x07070707))
require.Error(t, err)
assert.Contains(t, err.Error(), "mismatch, range: uint32 dimension: float32")
})
}
func TestQueryWithSubarrayOnFixedDimensions(t *testing.T) {
arrPath := createDenseIntegerGrid(t, 16)
cfg, err := NewConfig()
require.NoError(t, err)
tdbCtx, err := NewContext(cfg)
require.NoError(t, err)
// write the full grid
arr := openArray(t, arrPath, TILEDB_WRITE)
q, err := NewQuery(tdbCtx, arr)
require.NoError(t, err)
sa, err := arr.NewSubarray()
require.NoError(t, err)
err = sa.AddRange(0, MakeRange[uint8](0, 15))
require.NoError(t, err)
err = sa.AddRange(1, MakeRange[uint8](0, 15))
require.NoError(t, err)
err = q.SetSubarray(sa)
require.NoError(t, err)
data := make([]uint16, 16*16)
for i := range data {
data[i] = uint16(i)
}
_, err = q.SetDataBuffer("v", data)
require.NoError(t, err)
err = q.Submit()
require.NoError(t, err)
// read back the central inner 2x2 subgrid
arr = openArray(t, arrPath, TILEDB_READ)
q, err = NewQuery(tdbCtx, arr)
require.NoError(t, err)
sa, err = arr.NewSubarray()
require.NoError(t, err)
err = sa.AddRange(0, MakeRange[uint8](7, 8))
require.NoError(t, err)
err = sa.AddRange(1, MakeRange[uint8](7, 8))
require.NoError(t, err)
err = q.SetSubarray(sa)
require.NoError(t, err)
data = make([]uint16, 2*2)
_, err = q.SetDataBuffer("v", data)
require.NoError(t, err)
err = q.Submit()
require.NoError(t, err)
require.Equal(t, []uint16{119, 120, 135, 136}, data)
}
func TestQueryWithSubarrayOnVarDimensions(t *testing.T) {
arrPath := createSparse2dTable(t)
cfg, err := NewConfig()
require.NoError(t, err)
tdbCtx, err := NewContext(cfg)
require.NoError(t, err)
// write some values
arr := openArray(t, arrPath, TILEDB_WRITE)
q, err := NewQuery(tdbCtx, arr)
require.NoError(t, err)
_, err = q.SetDataBuffer("str", []byte("aaaabbbbccccdddd"))
require.NoError(t, err)
_, err = q.SetOffsetsBuffer("str", []uint64{0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15})
require.NoError(t, err)
_, err = q.SetDataBuffer("num", []float32{1.0, 2.0, 3.0, 4.0, 1.0, 2.0, 3.0, 4.0, 1.0, 2.0, 3.0, 4.0, 1.0, 2.0, 3.0, 4.0})
require.NoError(t, err)
_, err = q.SetDataBuffer("v", []uint16{0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15})
require.NoError(t, err)
require.NoError(t, q.Submit())
// read back the central inner 2x2 subgrid
arr = openArray(t, arrPath, TILEDB_READ)
q, err = NewQuery(tdbCtx, arr)
require.NoError(t, err)
sa, err := arr.NewSubarray()
require.NoError(t, err)
err = sa.AddRangeByName("str", MakeRange("b", "c"))
require.NoError(t, err)
err = sa.AddRangeByName("num", MakeRange[float32](2.0, 3.0))
require.NoError(t, err)
err = q.SetSubarray(sa)
require.NoError(t, err)
data := make([]uint16, 2*2)
_, err = q.SetDataBuffer("v", data)
require.NoError(t, err)
err = q.Submit()
require.NoError(t, err)
require.Equal(t, []uint16{5.0, 6.0, 9.0, 10.0}, data)
}
func createDenseIntegerGrid(t *testing.T, n uint8) string {
tileSize := uint8(4)
if n < 4 {
tileSize = n
}
arrPath := t.TempDir()
cfg, err := NewConfig()
require.NoError(t, err)
tdbCtx, err := NewContext(cfg)
require.NoError(t, err)
schema, err := NewArraySchema(tdbCtx, TILEDB_DENSE)
require.NoError(t, err)
domain, err := NewDomain(tdbCtx)
require.NoError(t, err)
yDim, err := NewDimension(tdbCtx, "y", TILEDB_UINT8, []uint8{0, n - 1}, tileSize)
require.NoError(t, err)
xDim, err := NewDimension(tdbCtx, "x", TILEDB_UINT8, []uint8{0, n - 1}, tileSize)
require.NoError(t, err)
require.NoError(t, domain.AddDimensions(yDim, xDim))
require.NoError(t, schema.SetDomain(domain))
vAttr, err := NewAttribute(tdbCtx, "v", TILEDB_UINT16)
require.NoError(t, err)
require.NoError(t, schema.AddAttributes(vAttr))
require.NoError(t, CreateArray(tdbCtx, arrPath, schema))
return arrPath
}
func createSparse2dTable(t *testing.T) string {
arrPath := t.TempDir()
cfg, err := NewConfig()
require.NoError(t, err)
tdbCtx, err := NewContext(cfg)
require.NoError(t, err)
schema, err := NewArraySchema(tdbCtx, TILEDB_SPARSE)
require.NoError(t, err)
domain, err := NewDomain(tdbCtx)
require.NoError(t, err)
sDim, err := NewStringDimension(tdbCtx, "str")
require.NoError(t, err)
nDim, err := NewDimension(tdbCtx, "num", TILEDB_FLOAT32, []float32{0.0, 100.0}, float32(4.0))
require.NoError(t, err)
require.NoError(t, domain.AddDimensions(sDim, nDim))
require.NoError(t, schema.SetDomain(domain))
vAttr, err := NewAttribute(tdbCtx, "v", TILEDB_UINT16)
require.NoError(t, err)
require.NoError(t, schema.AddAttributes(vAttr))
require.NoError(t, CreateArray(tdbCtx, arrPath, schema))
return arrPath
}
func openArray(t *testing.T, arrPath string, qt QueryType) *Array {
cfg, err := NewConfig()
require.NoError(t, err)
tdbCtx, err := NewContext(cfg)
require.NoError(t, err)
arr, err := NewArray(tdbCtx, arrPath)
require.NoError(t, err)
require.NoError(t, arr.Open(qt))
t.Cleanup(func() { arr.Close() })
return arr
}
func checkRange[T DimensionType](t *testing.T, r Range, start, end T) {
bounds, err := ExtractRange[T](r)
require.NoError(t, err)
require.Equal(t, 3, len(bounds))
assert.EqualValues(t, start, bounds[0])
assert.EqualValues(t, end, bounds[1])
assert.EqualValues(t, *new(T), bounds[2])
}