#' Create a \sQuote{batched} query object
#'
#' Batched queries return an initial result set even when it is incomplete. Where
#' the normal retrieval process will loop in place to complete a (potentially large)
#' result set, this function will return a result (which may be part of a larger
#' result set) allowing the user to assemble all part.
#'
#' The \code{tiledb_array} object can be parameterised as usual.
#'
#' @param x A \code{tiledb_array} object
#' @return A \code{batchedquery} object, that is a list containing an external pointer
#' to a TileDB Query object along with other support variables used by \code{fetchBatched}
#' @export
createBatched <- function(x) {
## add defaults, shortcut for now
i <- j <- k <- NULL
#verbose <- getOption("verbose", FALSE)
## ## deal with possible n-dim indexing
## ndlist <- nd_index_from_syscall(sys.call(), parent.frame())
## if (length(ndlist) >= 0) {
## if (length(ndlist) >= 1 && !is.null(ndlist[[1]])) i <- ndlist[[1]]
## if (length(ndlist) >= 2 && !is.null(ndlist[[2]])) j <- ndlist[[2]]
## if (length(ndlist) >= 3 && !is.null(ndlist[[3]])) k <- ndlist[[3]]
## if (length(ndlist) >= 4) message("Indices beyond the third dimension not supported in [i,j,k] form. Use selected_ranges().")
## }
ctx <- x@ctx
uri <- x@uri
sel <- x@attrs
sch <- tiledb::schema(x)
dom <- tiledb::domain(sch)
layout <- x@query_layout
asint64 <- x@datetimes_as_int64
enckey <- x@encryption_key
tstamp <- x@timestamp_end
sparse <- libtiledb_array_schema_sparse(sch@ptr)
dims <- tiledb::dimensions(dom)
dimnames <- sapply(dims, function(d) libtiledb_dim_get_name(d@ptr))
dimtypes <- sapply(dims, function(d) libtiledb_dim_get_datatype(d@ptr))
dimvarnum <- sapply(dims, function(d) libtiledb_dim_get_cell_val_num(d@ptr))
dimnullable <- sapply(dims, function(d) FALSE)
attrs <- tiledb::attrs(schema(x))
attrnames <- unname(sapply(attrs, function(a) libtiledb_attribute_get_name(a@ptr)))
attrtypes <- unname(sapply(attrs, function(a) libtiledb_attribute_get_type(a@ptr)))
attrvarnum <- unname(sapply(attrs, function(a) libtiledb_attribute_get_cell_val_num(a@ptr)))
attrnullable <- unname(sapply(attrs, function(a) libtiledb_attribute_get_nullable(a@ptr)))
if (length(sel)==1 && is.na(sel[1])) { # special case of NA selecting no attrs
attrnames <- character()
attrtypes <- character()
attrvarnum <- integer()
attrnullable <- logical()
}
if (length(sel) != 0 && !any(is.na(sel))) {
ind <- match(sel, attrnames)
if (length(ind) == 0) {
stop("Only non-existing columns selected.", call.=FALSE)
}
attrnames <- attrnames[ind]
attrtypes <- attrtypes[ind]
attrvarnum <- attrvarnum[ind]
attrnullable <- attrnullable[ind]
}
if (x@extended) { # if true return dimensions and attributes
allnames <- c(dimnames, attrnames)
alltypes <- c(dimtypes, attrtypes)
allvarnum <- c(dimvarnum, attrvarnum)
allnullable <- c(dimnullable, attrnullable)
} else { # otherwise only return attributes
allnames <- attrnames
alltypes <- attrtypes
allvarnum <- attrvarnum
allnullable <- attrnullable
}
## A preference can be set in a local per-user configuration file; if no value
## is set a fallback from the TileDB config object is used.
memory_budget <- get_allocation_size_preference()
spdl::debug("[createBatched] memory budget is {}", memory_budget)
if (length(enckey) > 0) {
if (length(tstamp) > 0) {
arrptr <- libtiledb_array_open_at_with_key(ctx@ptr, uri, "READ", enckey, tstamp)
} else {
arrptr <- libtiledb_array_open_with_key(ctx@ptr, uri, "READ", enckey)
}
} else {
if (length(tstamp) > 0) {
arrptr <- libtiledb_array_open_at(ctx@ptr, uri, "READ", tstamp)
} else {
arrptr <- libtiledb_array_open(ctx@ptr, uri, "READ")
}
}
if (length(x@timestamp_start) > 0) {
arrptr <- libtiledb_array_set_open_timestamp_start(arrptr, x@timestamp_start)
}
if (length(x@timestamp_end) > 0) {
arrptr <- libtiledb_array_set_open_timestamp_end(arrptr, x@timestamp_end)
}
if (length(x@timestamp_start) > 0 || length(x@timestamp_end) > 0) {
arrptr <- libtiledb_array_reopen(arrptr)
}
## helper function to sweep over names and types of domain
getDomain <- function(nm, tp) {
if (tp %in% c("ASCII", "CHAR")) {
libtiledb_array_get_non_empty_domain_var_from_name(arrptr, nm)
} else {
libtiledb_array_get_non_empty_domain_from_name(arrptr, nm, tp)
}
}
nonemptydom <- mapply(getDomain, dimnames, dimtypes, SIMPLIFY=FALSE)
## open query
qryptr <- libtiledb_query(ctx@ptr, arrptr, "READ")
qryptr <- libtiledb_query_set_layout(qryptr, if (isTRUE(nzchar(layout))) layout
else { if (sparse) "UNORDERED" else "COL_MAJOR" })
## ranges seem to interfere with the byte/element adjustment below so set up toggle
rangeunset <- TRUE
## ensure selected_ranges, if submitted, is of correct length
if (length(x@selected_ranges) != 0 &&
length(x@selected_ranges) != length(dimnames) &&
is.null(names(x@selected_ranges))) {
stop(paste0("If ranges are selected by index alone (and not named), ",
"one is required for each dimension."), call. = FALSE)
}
## expand a shorter-but-named selected_ranges list
if ( (length(x@selected_ranges) < length(dimnames))
&& (!is.null(names(x@selected_ranges))) ) {
fulllist <- vector(mode="list", length=length(dimnames))
ind <- match(names(x@selected_ranges), dimnames)
if (any(is.na(ind))) stop("Name for selected ranges does not match dimension names.")
for (ii in seq_len(length(ind))) {
fulllist[[ ind[ii] ]] <- x@selected_ranges[[ii]]
}
x@selected_ranges <- fulllist
}
## selected_ranges may be in different order than dimnames, so reorder if need be
if ((length(x@selected_ranges) == length(dimnames))
&& (!is.null(names(x@selected_ranges)))
&& (!identical(names(x@selected_ranges), dimnames))) {
x@selected_ranges <- x@selected_ranges[dimnames]
}
## if selected_ranges is still an empty list, make it an explicit one
if (length(x@selected_ranges) == 0) {
x@selected_ranges <- vector(mode="list", length=length(dimnames))
}
if (!is.null(i)) {
if (!is.null(x@selected_ranges[[1]])) {
stop("Cannot set both 'i' and first element of 'selected_ranges'.", call. = FALSE)
}
x@selected_ranges[[1]] <- i
}
if (!is.null(j)) {
if (!is.null(x@selected_ranges[[2]])) {
stop("Cannot set both 'j' and second element of 'selected_ranges'.", call. = FALSE)
}
x@selected_ranges[[2]] <- j
}
if (!is.null(k)) {
if (!is.null(x@selected_ranges[[3]])) {
stop("Cannot set both 'k' and second element of 'selected_ranges'.", call. = FALSE)
}
x@selected_ranges[[3]] <- k
}
## (i,j,k) are now done and transferred to x@select_ranges
## if ranges selected, use those
for (k in seq_len(length(x@selected_ranges))) {
sbrptr <- libtiledb_subarray(qryptr)
if (is.null(x@selected_ranges[[k]])) {
##cat("Adding null dim", k, "on", dimtypes[k], "\n")
vec <- .map2integer64(nonemptydom[[k]], dimtypes[k])
if (vec[1] != 0 && vec[2] != 0) { # corner case of A[] on empty array
sbrptr <- libtiledb_subarray_add_range_with_type(sbrptr, k-1L, dimtypes[k], vec[1], vec[2])
rangeunset <- FALSE
}
} else if (is.null(nrow(x@selected_ranges[[k]]))) {
##cat("Adding nrow null dim", k, "on", dimtypes[k], "\n")
vec <- x@selected_ranges[[k]]
vec <- .map2integer64(vec, dimtypes[k])
sbrptr <- libtiledb_subarray_add_range_with_type(sbrptr, k-1L, dimtypes[k], min(vec), max(vec))
rangeunset <- FALSE
} else {
##cat("Adding non-zero dim", k, "on", dimtypes[k], "\n")
m <- x@selected_ranges[[k]]
for (i in seq_len(nrow(m))) {
vec <- .map2integer64(c(m[i,1], m[i,2]), dimtypes[k])
sbrptr <- libtiledb_subarray_add_range_with_type(sbrptr, k-1L, dimtypes[k], vec[1], vec[2])
}
rangeunset <- FALSE
}
qryptr <- libtiledb_query_set_subarray_object(qryptr, sbrptr)
}
buflist <- vector(mode="list", length=length(allnames))
#if (!qryinit) {
## retrieve est_result_size
getEstimatedSize <- function(name, varnum, nullable, qryptr, datatype) {
if (is.na(varnum) && !nullable)
res <- libtiledb_query_get_est_result_size_var(qryptr, name)[1]
else if (is.na(varnum) && nullable)
res <- libtiledb_query_get_est_result_size_var_nullable(qryptr, name)[1]
else if (!is.na(varnum) && !nullable)
res <- libtiledb_query_get_est_result_size(qryptr, name)
else if (!is.na(varnum) && nullable)
res <- libtiledb_query_get_est_result_size_nullable(qryptr, name)[1]
if (rangeunset) {
sz <- tiledb_datatype_string_to_sizeof(datatype)
res <- res / sz
}
res
}
ressizes <- mapply(getEstimatedSize, allnames, allvarnum, allnullable, alltypes,
MoreArgs=list(qryptr=qryptr), SIMPLIFY=TRUE)
## ensure > 0 for correct handling of zero-length outputs, ensure respecting memory budget
resrv <- max(1, min(memory_budget/8, ressizes))
## allocate and set buffers
getBuffer <- function(name, type, varnum, nullable, resrv, qryptr, arrptr) {
if (is.na(varnum)) {
if (type %in% c("CHAR", "ASCII", "UTF8")) {
spdl::debug("[getBuffer] '{}' allocating 'char' {} rows given budget of {}", name, resrv, memory_budget)
buf <- libtiledb_query_buffer_var_char_alloc_direct(resrv, memory_budget, nullable)
qryptr <- libtiledb_query_set_buffer_var_char(qryptr, name, buf)
buf
} else {
message("Non-char var.num columns are not currently supported.")
}
} else {
spdl::debug("[getBuffer] '{}' allocating non-char {} rows given budget of {}", name, resrv, memory_budget)
buf <- libtiledb_query_buffer_alloc_ptr(type, resrv, nullable, varnum)
qryptr <- libtiledb_query_set_buffer_ptr(qryptr, name, buf)
buf
}
}
buflist <- mapply(getBuffer, allnames, alltypes, allvarnum, allnullable,
MoreArgs=list(resrv=resrv, qryptr=qryptr, arrptr=arrptr),
SIMPLIFY=FALSE)
## if we have a query condition, apply it
if (isTRUE(x@query_condition@init)) {
qryptr <- libtiledb_query_set_condition(qryptr, x@query_condition@ptr)
}
#}
res <- list(qryptr, allnames, allvarnum, alltypes, allnullable, buflist)
class(res) <- "batchedquery"
res
}
#' Run a \sQuote{batched} query
#'
#' Batched queries return an initial result set even when it is incomplete. Where
#' the normal retrieval process will loop in place to complete a (potentially large)
#' result set, this function will return a result (which may be part of a larger
#' result set) allowing the user to assemble all part.
#'
#' The \code{tiledb_array} object can be parameterised as usual.
#'
#' @param x A \code{tiledb_array} object
#' @param obj A \code{batchedquery} object as returned by \code{createBatched}
#' @return A data.frame object with the (potentially partial) result of a
#' batched query
#' @export
fetchBatched <- function(x, obj) {
stopifnot("The 'x' argument must be a 'tiledb_array'" = is(x, "tiledb_array"),
"The 'obj' argument must be 'batchedquery' object" = inherits(obj, "batchedquery"))
qryptr <- obj[[1]]
allnames <- obj[[2]]
allvarnum <- obj[[3]]
alltypes <- obj[[4]]
allnullable <- obj[[5]]
buflist <- obj[[6]]
asint64 <- x@datetimes_as_int64
#verbose <- getOption("verbose", FALSE)
## fire off query
qryptr <- libtiledb_query_submit(qryptr)
## check status
status <- libtiledb_query_status(qryptr)
##if (status != "COMPLETE") warning("Query returned '", status, "'.", call. = FALSE)
## close array
if (status == "COMPLETE") {
arrptr <- x@ptr
libtiledb_array_close(arrptr)
.pkgenv[["query_status"]] <- status
finished <- TRUE
}
## retrieve actual result size (from fixed size element columns)
getResultSize <- function(name, varnum, qryptr) {
if (is.na(varnum)) # symbols come up with higher count
libtiledb_query_result_buffer_elements(qryptr, name, 0)
else
libtiledb_query_result_buffer_elements(qryptr, name)
}
estsz <- mapply(getResultSize, allnames, allvarnum, MoreArgs=list(qryptr=qryptr), SIMPLIFY=TRUE)
spdl::debug("[fetchBatched] estimated result sizes {}", paste(estsz, collapse=","))
if (any(!is.na(estsz))) {
resrv <- max(estsz, na.rm=TRUE)
} else {
resrv <- resrv/8 # character case where bytesize of offset vector was used
}
spdl::debug("[fetchBatched] expected size {}", resrv)
## Permit one pass to allow zero-row schema read
#if (resrv == 0 && counter > 1L) {
#finished <- TRUE
##if (verbose) message("Breaking loop at zero length expected")
#if (status != "COMPLETE") warning("Query returned '", status, "'.", call. = FALSE)
#.pkgenv[["query_status"]] <- status
#break
#}
## get results
getResult <- function(buf, name, varnum, estsz, qryptr) {
has_dumpbuffers <- length(x@dumpbuffers) > 0
if (is.na(varnum)) {
vec <- libtiledb_query_result_buffer_elements_vec(qryptr, name)
if (has_dumpbuffers) {
vlcbuf_to_shmem(x@dumpbuffers, name, buf, vec)
}
libtiledb_query_get_buffer_var_char(buf, vec[1], vec[2])[,1][seq_len(estsz)]
} else {
if (has_dumpbuffers) {
vecbuf_to_shmem(x@dumpbuffers, name, buf, estsz, varnum)
}
libtiledb_query_get_buffer_ptr(buf, asint64)[seq_len(estsz)]
}
}
reslist <- mapply(getResult, buflist, allnames, allvarnum, estsz,
MoreArgs=list(qryptr=qryptr), SIMPLIFY=FALSE)
## convert list into data.frame (possibly dealing with list columns) and subset
vnum <- 1 # default value of variable number of elements per cell
if (is.list(allvarnum)) allvarnum <- unlist(allvarnum)
if (length(allvarnum) > 0 && any(!is.na(allvarnum))) vnum <- max(allvarnum, na.rm=TRUE)
if (is.finite(vnum) && (vnum > 1)) {
## turn to list col if a varnum != 1 (and not NA) seen
ind <- which(allvarnum != 1 & !is.na(allvarnum))
for (k in ind) {
ncells <- allvarnum[k]
v <- reslist[[k]]
## we split a vector v into 'list-columns' which element containing
## ncells value (and we get ncells from the Array schema)
## see https://stackoverflow.com/a/9547594/143305 for I()
## and https://stackoverflow.com/a/3321659/143305 for split()
reslist[[k]] <- I(unname(split(v, ceiling(seq_along(v)/ncells))))
}
}
res <- data.frame(reslist)[seq_len(resrv),,drop=FALSE]
colnames(res) <- allnames
spdl::debug("[fetchBatched] retrieved {}", paste(dim(res), collapse="x"))
##overallresults[[counter]] <- res
##counter <- counter + 1L
res
}
#' Return \sQuote{batched} status
#'
#' Batched queries return an initial result set even when it is incomplete. Where
#' the normal retrieval process will loop in place to complete a (potentially large)
#' result set, this function will return a result (which may be part of a larger
#' result set) allowing the user to assemble all part.
#'
#' @param obj A list object as returned by \code{createBatched}
#' @return The Query status as a character variable
#' @export
statusBatched <- function(obj) {
stopifnot("The 'obj' argument must be 'batchedquery' object" = inherits(obj, "batchedquery"))
libtiledb_query_status(obj[[1]])
}
#' Check \sQuote{batched} query for completion
#'
#' Batched queries return an initial result set even when it is incomplete. Where
#' the normal retrieval process will loop in place to complete a (potentially large)
#' result set, this function will return a result (which may be part of a larger
#' result set) allowing the user to assemble all part.
#'
#' @param obj A list object as returned by \code{createBatched}
#' @return A logical value to indicated if the query completed
#' @export
completedBatched <- function(obj) {
stopifnot("The 'obj' argument must be 'batchedquery' object" = inherits(obj, "batchedquery"))
libtiledb_query_status(obj[[1]]) == "COMPLETE"
}
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