inst/tinytest/test_arrayschemaevolution.R

In TileDB-Inc/TileDB-R: Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays

library(tinytest)
library(tiledb)

if (Sys.info()[["sysname"]] == "Windows") exit_file("Skip on Windows")

ctx <- tiledb_ctx(limitTileDBCores())

if (tiledb_version(TRUE) < "2.11.0") exit_file("Needs TileDB 2.11.* or later")

df <- data.frame(key=letters[1:10],
                 val=1:10)
uri <- tempfile()
arr <- fromDataFrame(df, uri)

ase <- tiledb_array_schema_evolution()
attr <- tiledb_attr("foo", "INT32")
ase <- tiledb_array_schema_evolution_add_attribute(ase, attr)
ase <- tiledb_array_schema_evolution_array_evolve(ase, uri)
arr <- tiledb_array(uri, return_as="data.frame", extended=FALSE)
res <- arr[]
expect_equal(dim(res), c(10,3))
expect_equal(colnames(res), c("key", "val", "foo"))

ase <- tiledb_array_schema_evolution()
ase <- tiledb_array_schema_evolution_drop_attribute(ase, "val")
ase <- tiledb_array_schema_evolution_array_evolve(ase, uri)
arr <- tiledb_array(uri, return_as="data.frame", extended=FALSE)
res <- arr[]
expect_equal(dim(res), c(10,2))
expect_equal(colnames(res), c("key", "foo"))


if (tiledb_version(TRUE) < "2.17.0") exit_file("Needs TileDB 2.17.* or later")

df <- data.frame(key=letters[1:10], val=c(1:5,5:1))
uri <- tempfile()
arr <- fromDataFrame(df, uri)

sch <- schema(uri)
attrs <- attrs(sch)
attr <- attrs$val   # copy of attribute

## First drop existing attribute
ase <- tiledb_array_schema_evolution()
ase <- tiledb_array_schema_evolution_drop_attribute(ase, "val")
tiledb_array_schema_evolution_array_evolve(ase, uri)

## Second add enumeration under a name
ase <- tiledb_array_schema_evolution()
enums <- c("blue", "green", "orange", "pink", "red")
ase <- tiledb_array_schema_evolution_add_enumeration(ase, "frobo", enums)

## Third connect the attribute to the enum and add it back in
attr <- tiledb_attribute_set_enumeration_name(attr, "frobo")
ase <- tiledb_array_schema_evolution_add_attribute(ase, attr)
tiledb_array_schema_evolution_array_evolve(ase, uri)

## check as data.frame
arr <- tiledb_array(uri, return_as="data.frame")
res <- arr[]
expect_true(is.factor(res$val))
expect_equal(levels(res$val), enums)
expect_equal(as.integer(res$val), c(1:5,5:1))


## -- testing 'create empty following by extending'
if (tiledb_version(TRUE) < "2.17.3") exit_file("Needs TileDB 2.17.3 or later")
uri <- tempfile()
dom <- tiledb_domain(dims = tiledb_dim("rows", c(1L, 20L), 10L, "INT32"))
attrs <- c(tiledb_attr("a", type = "INT32"), tiledb_attr("b", type = "INT32"))
schema <- tiledb_array_schema(dom, attrs = attrs, sparse = TRUE)
schema <- tiledb_array_schema_set_enumeration_empty(schema, attrs[[2]], "an_enum")
tiledb_array_create(uri, schema)
df <- data.frame(rows = 1:10, a = 100 + 0:9, b = rep(c(1L, 2L), each=5))
A <- tiledb_array(uri)
A[] <- df
arr <- tiledb_array(uri, return_as="data.frame")[]
expect_true(is.factor(arr[, "b"]))
expect_equal(levels(arr[, "b"]), character()) # empty levels vector
## now alter array
ase <- tiledb_array_schema_evolution()
arr <- tiledb_array(uri)
arr <- tiledb_array_open(arr, "READ")
ase <- tiledb_array_schema_evolution_extend_enumeration(ase, arr, "an_enum", c("red", "green"))
tiledb_array_schema_evolution_array_evolve(ase, uri)
arr <- tiledb_array(uri, return_as="data.frame")[]
expect_equal(levels(arr[, "b"]), c("red", "green"))
## append to array
df <- data.frame(rows = 11:20, a = 100 + 10:19, b = rep(c(3L, 4L), each=5))
A <- tiledb_array(uri)
A[] <- df
## and alter again
ase <- tiledb_array_schema_evolution()
arr <- tiledb_array(uri)
arr <- tiledb_array_open(arr, "READ")
ase <- tiledb_array_schema_evolution_extend_enumeration(ase, arr, "an_enum", c("blue", "orange"))
tiledb_array_schema_evolution_array_evolve(ase, uri)
arr <- tiledb_array(uri, return_as="data.frame")[]
expect_equal(levels(arr[, "b"]), c("red", "green", "blue", "orange"))


## -- testing query condition on non int32 columns
run_int_col_test <- function(coltype) {
    uri <- tempfile()
    enums <- c("blue", "green", "red")
    dom <- tiledb_domain(dims = tiledb_dim(name="dim", domain=c(0L,100L), tile=10L, type="INT32"))
    attrs <- c(tiledb_attr(name="fct", type = coltype, enumeration=enums),
               tiledb_attr(name="dbl", type = "FLOAT64"))
    schema <- tiledb_array_schema(domain=dom, attrs=attrs, sparse=TRUE, enumerations=list(fct=enums))
    tiledb_array_create(uri, schema)

    set.seed(42)
    df <- data.frame(dim = 1:10, fct = sample(length(enums), 10, replace=TRUE) - 1, dbl = rnorm(10))
    arr <- tiledb_array(uri)
    arr[] <- df

    res <- tiledb_array(uri, return_as="data.frame", query_condition = parse_query_condition(fct == blue, arr))[]
    expect_equal(nrow(res), 5)

    res <- tiledb_array(uri, return_as="data.frame", query_condition = parse_query_condition(fct == green, arr))[]
    expect_equal(nrow(res), 3)

    res <- tiledb_array(uri, return_as="data.frame", query_condition = parse_query_condition(fct == red, arr))[]
    expect_equal(nrow(res), 2)

    res <- tiledb_array(uri, return_as="data.frame", query_condition = parse_query_condition(fct != blue, arr))[]
    expect_equal(nrow(res), 5)

    expect_error(tiledb_array(uri, return_as="data.frame", query_condition = parse_query_condition(fct > blue, arr))[])

    unlink(uri)
}
sapply(c("INT8", "INT16", "INT32", "UINT8", "UINT16", "UINT32"), run_int_col_test)


## test that factor levels can grow without overlap
uri <- tempfile()
df1 <- data.frame(id = 1:3, obs = factor(c("A", "B", "A")))
fromDataFrame(df1, uri, col_index=1, tile_domain=c(1L, 6L))

## write with a factor with two elements but without one of the initial ones
## while factor(c("B", "C", "B")) gets encoded as c(1,2,1) it should really
## encoded as c(2,3,2) under levels that are c("A", "B", "C") -- and the
## write method now does that
df2 <- data.frame(id = 4:6, obs = factor(c("B", "C", "B")))
fromDataFrame(df2, uri, col_index=1, mode="append")

res <- tiledb_array(uri, return_as="data.frame")[]

expect_equal(nrow(res), 6)
expect_equal(nlevels(res[["obs"]]), 3)
expect_equal(levels(res[["obs"]]), c("A", "B", "C"))
expect_equal(as.integer(res[["obs"]]), c(1L, 2L, 1L, 2L, 3L, 2L))

ref <- rbind(df1, df2)
expect_equivalent(res, ref) # equivalent because of query status attribute


## test that ordered factor levels can grow without overlap
uri <- tempfile()
df1 <- data.frame(id = 1:3, obs = ordered(c("A", "B", "A")))
fromDataFrame(df1, uri, col_index=1, tile_domain=c(1L, 6L))

## write with a factor with two elements but without one of the initial ones
## while factor(c("B", "C", "B")) gets encoded as c(1,2,1) it should really
## encoded as c(2,3,2) under levels that are c("A", "B", "C") -- and the
## write method now does that
df2 <- data.frame(id = 4:6, obs = ordered(c("B", "C", "B")))
fromDataFrame(df2, uri, col_index=1, mode="append")

res <- tiledb_array(uri, return_as="data.frame")[]

expect_equal(nrow(res), 6)
expect_equal(nlevels(res[["obs"]]), 3)
expect_equal(levels(res[["obs"]]), c("A", "B", "C"))
expect_equal(as.integer(res[["obs"]]), c(1L, 2L, 1L, 2L, 3L, 2L))

ref <- rbind(df1, df2)
expect_equivalent(res, ref) # equivalent because of query status attribute


## another test for growing
uri <- tempfile()
df1 <- data.frame(rows=11:14, a=200+0:3, b=factor(rep(c("blue", "ornage"), each=2)))
expect_silent(fromDataFrame(df1, uri, col_index=1, tile_domain=c(1L, 30L)))
df2 <- data.frame(rows=21:24, a=300+0:3, b=factor(rep(c("brown", "yellow"), each=2)))
expect_silent(fromDataFrame(df2, uri, mode="append", col_index=1))

res <- tiledb_array(uri, return_as="data.frame")[]
expect_equivalent(res, rbind(df1, df2))   # factors in data.frame get releveled too

## check factor additions do not overflow
for (tp in c("INT8", "UINT8")) {
    uri <- tempfile()

    dom <- tiledb_domain(dims = tiledb_dim("rows", c(1L, 300L), 10L, "INT32"))
    attrs <- c(tiledb_attr("a", type = "INT32"),
               tiledb_attr("b", type = tp))
    schema <- tiledb_array_schema(dom, attrs = attrs, sparse = TRUE)
    schema <- tiledb_array_schema_set_enumeration_empty(schema, attrs[[2]], "b")
    invisible(tiledb_array_create(uri, schema))

    df <- data.frame(rows = 1:50, a = 100 + 0:49, b = factor(paste0("f", 101:150)))
    expect_silent(fromDataFrame(df, uri, mode="append", col_index=1))

    df <- data.frame(rows = 51:130, a = 200 + 0:79, b = factor(paste0("f", 151:230)))
    if (tp == "INT8") {
        expect_error(fromDataFrame(df, uri, mode="append", col_index=1))	# errors for INT8
    } else {
        expect_silent(fromDataFrame(df, uri, mode="append", col_index=1)) 	# passes for UINT8
    }
}

## tests formerly in file 'test_arrayschemaevolution_arrow.R'
if (Sys.info()[["sysname"]] == "Windows") exit_file("Skip on Windows")
if (Sys.getenv("CI", "") == "") exit_file("Skip unextended test run")

if (tiledb_version(TRUE) < "2.17.0") exit_file("Needs TileDB 2.17.* or later")

df <- data.frame(key=letters[1:10], val=c(1:5,5:1))
uri <- tempfile()
arr <- fromDataFrame(df, uri)

sch <- schema(uri)
attrs <- attrs(sch)
attr <- attrs$val   # copy of attribute

## First drop existing attribute
ase <- tiledb_array_schema_evolution()
ase <- tiledb_array_schema_evolution_drop_attribute(ase, "val")
tiledb_array_schema_evolution_array_evolve(ase, uri)

## Second add enumeration under a name
ase <- tiledb_array_schema_evolution()
enums <- c("blue", "green", "orange", "pink", "red")
ase <- tiledb_array_schema_evolution_add_enumeration(ase, "frobo", enums)

## Third connect the attribute to the enum and add it back in
attr <- tiledb_attribute_set_enumeration_name(attr, "frobo")
ase <- tiledb_array_schema_evolution_add_attribute(ase, attr)
tiledb_array_schema_evolution_array_evolve(ase, uri)

## check as data.frame
arr <- tiledb_array(uri, return_as="data.frame")
res <- arr[]
expect_true(is.factor(res$val))
expect_equal(levels(res$val), enums)
expect_equal(as.integer(res$val), c(1:5,5:1))

## check as arrow
if (!requireNamespace("arrow", quietly=TRUE)) exit_file("No 'arrow' package.")
arr <- tiledb_array(uri, return_as="arrow")
res <- arr[]
v <- res[["val"]]$as_vector()
expect_true(is.factor(v))
expect_equal(levels(v), enums)
expect_equal(as.integer(v), c(1:5,5:1))

## current domain
if (tiledb_version(TRUE) < "2.26.0") exit_file("Needs TileDB 2.26.* or later")
uri <- tempfile()
dim <- tiledb_dim("dim", c(1L, 1000L), 50L, type = "INT32")
dom <- tiledb_domain(dim = dim)
attr <- tiledb_attr("a", type = "INT32")
sch <- tiledb_array_schema(dom, attrs = attr, sparse = TRUE)
arr <- tiledb_array_create(uri, sch)
cd <- tiledb_current_domain()
ndr <- tiledb_ndrectangle(dom)
tiledb_ndrectangle_set_range(ndr, "dim", 1L, 100L)
cd <- tiledb_current_domain_set_ndrectangle(cd, ndr)
ase <- tiledb_array_schema_evolution()
expect_silent(tiledb_array_schema_evolution_expand_current_domain(ase, cd))
expect_silent(tiledb_array_schema_evolution_array_evolve(ase, uri))