TileDBArray.R

#  MIT License
#
#  Copyright (c) 2017-2025 TileDB Inc.
#
#  Permission is hereby granted, free of charge, to any person obtaining a copy
#  of this software and associated documentation files (the "Software"), to deal
#  in the Software without restriction, including without limitation the rights
#  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
#  copies of the Software, and to permit persons to whom the Software is
#  furnished to do so, subject to the following conditions:
#
#  The above copyright notice and this permission notice shall be included in all
#  copies or substantial portions of the Software.
#
#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
#  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
#  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
#  SOFTWARE.


#' An S4 class for a TileDB Array
#'
#' This class replaces the earlier (and now removed) \code{tiledb_dense}
#' and \code{tiledb_sparse} and provides equivalent functionality
#' based on a refactored implementation utilising newer TileDB features.
#'
#' @slot ctx A TileDB context object
#' @slot uri A character description with the array URI
#' @slot is.sparse A logical value whether the array is sparse or not
#' @slot attrs A character vector to select particular column
#' \sQuote{attributes}; default is an empty character vector implying
#' \sQuote{all} columns, the special value \code{NA_character_} has the opposite
#' effect and selects \sQuote{none}.
#' @slot extended A logical value, defaults to \code{TRUE}, indicating whether
#' index columns are returned as well.
#' @slot selected_ranges An optional list with matrices where each matrix i
#' describes the (min,max) pair of ranges for dimension i
#' @slot selected_points An optional list with vectors where each vector i
#' describes the selected points for dimension i
#' @slot query_layout An optional character value
#' @slot datetimes_as_int64 A logical value
#' @slot encryption_key A character value
#' @slot query_condition A Query Condition object
#' @slot timestamp_start A POSIXct datetime variable for the inclusive
#' interval start
#' @slot timestamp_end A POSIXct datetime variable for the inclusive
#' interval start
#' @slot return_as A character value with the desired \code{tiledb_array}
#' conversion, permitted values are \sQuote{asis} (default, returning a list
#' of columns), \sQuote{array}, \sQuote{matrix},\sQuote{data.frame},
#' \sQuote{data.table} \sQuote{tibble}, \sQuote{arrow_table} or \sQuote{arrow}
#' (where the last two are synonyms); note that \sQuote{data.table},
#' \sQuote{tibble} and \sQuote{arrow} require the respective packages
#' to be installed.
#' @slot query_statistics A logical value, defaults to \sQuote{FALSE}; if
#' \sQuote{TRUE} the query statistics are returned (as a JSON string) via the
#' attribute \sQuote{query_statistics} of the return object.
#' @slot sil An optional and internal list object with schema information, used
#' for parsing queries.
#' @slot dumpbuffers An optional character variable with a directory name
#' (relative to \code{/dev/shm}) for writing out results buffers (for internal
#' use / testing)
#' @slot buffers An optional list with full pathnames of shared memory buffers
#' to read data from
#' @slot strings_as_factors An optional logical to convert character columns to
#' factor type
#' @slot keep_open An optional logical to not close after read or write
#' @slot ptr External pointer to the underlying implementation
#' @exportClass tiledb_array
setClass(
  "tiledb_array",
  slots = list(
    ctx = "tiledb_ctx",
    uri = "character",
    is.sparse = "logical",
    attrs = "character",
    extended = "logical",
    selected_ranges = "list",
    selected_points = "list",
    query_layout = "character",
    datetimes_as_int64 = "logical",
    encryption_key = "character",
    query_condition = "tiledb_query_condition",
    timestamp_start = "POSIXct",
    timestamp_end = "POSIXct",
    return_as = "character",
    query_statistics = "logical",
    strings_as_factors = "logical",
    keep_open = "logical",
    sil = "list",
    dumpbuffers = "character",
    buffers = "list",
    ptr = "externalptr"
  )
)

#' Constructs a tiledb_array object backed by a persisted tiledb array uri
#'
#' tiledb_array returns a new object. This class is experimental.
#'
#' @param uri uri path to the tiledb array
#' @param query_type optionally loads the array in "READ" or "WRITE" only modes.
#' @param is.sparse optional logical switch, defaults to "NA"
#' letting array determine it
#' @param attrs optional character vector to select attributes, default is
#' empty implying all are selected, the special value \code{NA_character_}
#' has the opposite effect and implies no attributes are returned.
#' @param extended optional logical switch selecting wide \sQuote{data.frame}
#' format, defaults to \code{TRUE}
#' @param selected_ranges optional A list with matrices where each matrix i
#' describes the (min,max) pair of ranges selected for dimension i
#' @param selected_points optional A list with vectors where each vector i
#' describes the points selected in dimension i
#' @param query_layout optional A value for the TileDB query layout, defaults to
#' an empty character variable indicating no special layout is set
#' @param datetimes_as_int64 optional A logical value selecting date  and
#' datetime value representation as \sQuote{raw} \code{integer64} and not as
#' \code{Date}, \code{POSIXct} or \code{nanotime} objects.
#' @param encryption_key optional A character value with an AES-256 encryption
#' key in case the array was written with encryption.
#' @param query_condition optional \code{tiledb_query_condition} object, by
#' default uninitialized without a condition; this functionality requires
#' TileDB 2.3.0 or later
#' @param timestamp_start optional A POSIXct Datetime value determining the
#' inclusive time point at which the array is to be opened. No fragments
#' written earlier will be considered.
#' @param timestamp_end optional A POSIXct Datetime value determining the
#' inclusive time point until which the array is to be opened. No fragments
#' written earlier later be considered.
#' @param return_as optional A character value with the desired
#' \code{tiledb_array} conversion, permitted values are \sQuote{asis} (default,
#' returning a list of columns), \sQuote{array}, \sQuote{matrix},
#' \sQuote{data.frame}, \sQuote{data.table}, \sQuote{tibble},
#' \sQuote{arrow_table}, or \sQuote{arrow} (as an alias for
#' \sQuote{arrow_table}; here \sQuote{data.table}, \sQuote{tibble} and
#' \sQuote{arrow} require the respective packages to be installed.
#' The existing \code{as.*} arguments take precedent over this.
#' @param query_statistics optional A logical value, defaults to \sQuote{FALSE};
#' if \sQuote{TRUE} the query statistics are returned (as a JSON string) via
#' the attribute \sQuote{query_statistics} of the return object.
#' @param strings_as_factors An optional logical to convert character columns to
#' factor type; defaults to the value of
#' \code{getOption("stringsAsFactors", FALSE)}.
#' @param keep_open An optional logical to not close after read or write
#' @param sil optional A list, by default empty to store schema information
#' when query objects are parsed.
#' @param dumpbuffers An optional character variable with a directory name
#' (relative to \code{/dev/shm}) for writing out results buffers (for
#' internal use / testing)
#' @param buffers An optional list with full pathnames of shared memory buffers
#' to read data from
#' @param ctx optional tiledb_ctx
#' @param as.data.frame An optional deprecated alternative to
#' \code{return_as="data.frame"} which has been deprecated and removed, but is
#' still used in one BioConductor package; this argument will be removed
#' once the updated package has been released.
#' @return tiledb_array object
#' @importFrom spdl set_level
#' @export
tiledb_array <- function(
  uri,
  query_type = c("READ", "WRITE"),
  is.sparse = NA,
  attrs = character(),
  extended = TRUE,
  selected_ranges = list(),
  selected_points = list(),
  query_layout = character(),
  datetimes_as_int64 = FALSE,
  encryption_key = character(),
  query_condition = new("tiledb_query_condition"),
  timestamp_start = as.POSIXct(double(), origin = "1970-01-01"),
  timestamp_end = as.POSIXct(double(), origin = "1970-01-01"),
  return_as = get_return_as_preference(),
  query_statistics = FALSE,
  strings_as_factors = getOption("stringsAsFactors", FALSE),
  keep_open = FALSE,
  sil = list(),
  dumpbuffers = character(),
  buffers = list(),
  ctx = tiledb_get_context(),
  as.data.frame = FALSE
) {
  stopifnot(
    "Argument 'ctx' must be a tiledb_ctx object" = is(ctx, "tiledb_ctx"),
    "Argument 'uri' must be a string scalar" = !missing(uri) && is.scalar(uri, "character"),
    "Argument 'matrix' (for 'return_as') cannot be selected for sparse arrays" =
      !(isTRUE(is.sparse) && return_as == "matrix")
  )
  query_type <- match.arg(query_type)
  spdl::debug("[tiledb_array] query is {}", query_type)
  if (length(encryption_key) > 0) {
    stopifnot("if used, argument aes_key must be character" = is.character(encryption_key))
    array_xptr <- libtiledb_array_open_with_key(ctx@ptr, uri, query_type, encryption_key)
  } else {
    array_xptr <- libtiledb_array_open(ctx@ptr, uri, query_type)
  }

  if (as.data.frame) {
    ## accommodating TileDBArray prior to BioConductor 3.20
    .Deprecated(old = "as.data.frame", new = r"(return_as="data.frame")")
    return_as <- "data.frame"
  }

  if (length(timestamp_start) > 0) {
    libtiledb_array_set_open_timestamp_start(array_xptr, timestamp_start)
  }
  if (length(timestamp_end) > 0) {
    libtiledb_array_set_open_timestamp_end(array_xptr, timestamp_end)
  }

  schema_xptr <- libtiledb_array_get_schema(array_xptr)
  is_sparse_status <- libtiledb_array_schema_sparse(schema_xptr)
  if (!is.na(is.sparse) && is.sparse != is_sparse_status) {
    libtiledb_array_close(array_xptr)
    if (is_sparse_status) {
      stop("dense array selected but sparse array found", call. = FALSE)
    } else {
      stop("sparse array selected but dense array found", call. = FALSE)
    }
  }
  is.sparse <- is_sparse_status
  if (!keep_open) array_xptr <- libtiledb_array_close(array_xptr)
  new("tiledb_array",
    ctx = ctx,
    uri = uri,
    is.sparse = is.sparse,
    attrs = attrs,
    extended = extended,
    selected_ranges = selected_ranges,
    selected_points = selected_points,
    query_layout = query_layout,
    datetimes_as_int64 = datetimes_as_int64,
    encryption_key = encryption_key,
    query_condition = query_condition,
    timestamp_start = timestamp_start,
    timestamp_end = timestamp_end,
    return_as = return_as,
    query_statistics = query_statistics,
    strings_as_factors = strings_as_factors,
    keep_open = keep_open,
    sil = sil,
    dumpbuffers = dumpbuffers,
    buffers = buffers,
    ptr = array_xptr
  )
}

#' Return a schema from a tiledb_array object
#'
#' @param object tiledb array object
#' @param ... Extra parameter for function signature, currently unused
#' @return The schema for the object
setMethod("schema", "tiledb_array", function(object, ...) {
  ctx <- object@ctx
  uri <- object@uri
  enckey <- object@encryption_key
  if (length(enckey) > 0) {
    schema_xptr <- libtiledb_array_schema_load_with_key(ctx@ptr, uri, enckey)
  } else {
    schema_xptr <- libtiledb_array_schema_load(ctx@ptr, uri)
  }
  return(tiledb_array_schema.from_ptr(schema_xptr, object@ptr))
})

## unexported helper function to deal with ... args / enckey in next method
.array_schema_load <- function(ctxptr, uri, enckey = character()) {
  if (length(enckey) > 0) {
    schema_xptr <- libtiledb_array_schema_load_with_key(ctxptr, uri, enckey)
  } else {
    schema_xptr <- libtiledb_array_schema_load(ctxptr, uri)
  }
}
.array_open <- function(ctxptr, uri, enckey = character()) {
  if (length(enckey) > 0) {
    arr_xptr <- libtiledb_array_open_with_key(ctxptr, uri, "READ", enckey)
  } else {
    arr_xptr <- libtiledb_array_open(ctxptr, uri, "READ")
  }
}

#' Return a schema from a URI character value
#'
#' @param object A character variable with a URI
#' @param ... Extra parameters such as \sQuote{enckey}, the encryption key
#' @return The schema for the object
setMethod("schema", "character", function(object, ...) {
  ctx <- tiledb_get_context()
  schema_xptr <- .array_schema_load(ctx@ptr, object, ...)
  array_xptr <- .array_open(ctx@ptr, object, ...)
  return(tiledb_array_schema.from_ptr(schema_xptr, array_xptr))
})


#' Prints a tiledb_array object
#'
#' @param object A tiledb array object
#' @export
setMethod(
  "show",
  signature = "tiledb_array",
  definition = function(object) {
    cat("tiledb_array\n",
      "  uri                = '", object@uri, "'\n",
      "  schema_version     = ", tiledb_array_schema_version(schema(object)), "\n",
      "  is.sparse          = ", if (object@is.sparse) "TRUE" else "FALSE", "\n",
      "  attrs              = ", if (length(object@attrs) == 0) {
        "(none)"
      } else {
        paste(object@attrs, collapse = ",")
      }, "\n",
      "  selected_ranges    = ", if (length(object@selected_ranges) > 0) {
        sprintf("(%d non-null sets)", sum(sapply(object@selected_ranges, function(x) !is.null(x))))
      } else {
        "(none)"
      }, "\n",
      "  selected_points    = ", if (length(object@selected_points) > 0) {
        sprintf("(%d non-null points)", sum(sapply(object@selected_points, function(x) !is.null(x))))
      } else {
        "(none)"
      }, "\n",
      "  extended           = ", if (object@extended) "TRUE" else "FALSE", "\n",
      "  query_layout       = ", if (length(object@query_layout) == 0) "(none)" else object@query_layout, "\n",
      "  datetimes_as_int64 = ", if (object@datetimes_as_int64) "TRUE" else "FALSE", "\n",
      "  encryption_key     = ", if (length(object@encryption_key) == 0) "(none)" else "(set)", "\n",
      "  query_condition    = ", if (isTRUE(object@query_condition@init)) "(set)" else "(none)", "\n",
      "  timestamp_start    = ", if (length(object@timestamp_start) == 0) "(none)" else format(object@timestamp_start), "\n",
      "  timestamp_end      = ", if (length(object@timestamp_end) == 0) "(none)" else format(object@timestamp_end), "\n",
      "  return_as          = '", object@return_as, "'\n",
      "  query_statistics   = ", if (object@query_statistics) "TRUE" else "FALSE", "\n",
      "  strings_as_factors = ", if (object@strings_as_factors) "TRUE" else "FALSE", "\n",
      "  keep_open          = ", if (object@keep_open) "TRUE" else "FALSE", "\n",
      sep = ""
    )
  }
)

setValidity("tiledb_array", function(object) {
  msg <- NULL
  valid <- TRUE

  if (!is(object@ctx, "tiledb_ctx")) {
    valid <- FALSE
    msg <- c(msg, "The 'ctx' slot does not contain a ctx object.")
  }

  if (!is.character(object@uri)) {
    valid <- FALSE
    msg <- c(msg, "The 'uri' slot does not contain a character value.")
  }

  if (!is.logical(object@is.sparse)) {
    valid <- FALSE
    msg <- c(msg, "The 'is.sparse' slot does not contain a logical value.")
  }

  if (!is.character(object@attrs)) {
    valid <- FALSE
    msg <- c(msg, "The 'attrs' slot does not contain a character vector.")
  }

  if (!is.logical(object@extended)) {
    valid <- FALSE
    msg <- c(msg, "The 'extended' slot does not contain a logical value.")
  }

  if (!is.list(object@selected_ranges)) {
    valid <- FALSE
    msg <- c(msg, "The 'selected_ranges' slot does not contain a list.")
  } else {
    for (i in (seq_len(length(object@selected_ranges)))) {
      if (!is.null(object@selected_ranges[[i]])) {
        if (length(dim(object@selected_ranges[[i]])) != 2) {
          valid <- FALSE
          msg <- c(msg, sprintf("Element '%d' of 'selected_ranges' is not 2-d.", i))
        }
        if (ncol(object@selected_ranges[[i]]) != 2) {
          valid <- FALSE
          msg <- c(msg, sprintf("Element '%d' of 'selected_ranges' is not two column.", i))
        }
      }
    }
  }

  if (!is.list(object@selected_points)) {
    valid <- FALSE
    msg <- c(msg, "The 'selected_points' slot does not contain a list.")
  } else {
    for (i in (seq_len(length(object@selected_points)))) {
      if (!is.null(object@selected_points[[i]])) {
        if (!is.vector(object@selected_points[[i]]) && !inherits(object@selected_points[[i]], "integer64")) {
          valid <- FALSE
          msg <- c(msg, sprintf("Element '%d' of 'selected_points' is not a vector.", i))
        }
      }
    }
  }

  if (!is.character(object@query_layout)) {
    valid <- FALSE
    msg <- c(msg, "The 'query_layout' slot does not contain a character value.")
  }

  if (!is.logical(object@datetimes_as_int64)) {
    valid <- FALSE
    msg <- c(msg, "The 'datetimes_as_int64' slot does not contain a logical value.")
  }

  if (!is.character(object@encryption_key)) {
    valid <- FALSE
    msg <- c(msg, "The 'encryption_key' slot does not contain a character vector.")
  }

  if (!is(object@query_condition, "tiledb_query_condition")) {
    valid <- FALSE
    msg <- c(msg, "The 'query_condition' slot does not contain a query condition object.")
  }

  if (!inherits(object@timestamp_start, "POSIXct")) {
    valid <- FALSE
    msg <- c(msg, "The 'timestamp_start' slot does not contain a POSIXct value.")
  }

  if (!inherits(object@timestamp_end, "POSIXct")) {
    valid <- FALSE
    msg <- c(msg, "The 'timestamp_end' slot does not contain a POSIXct value.")
  }

  if (!is(object@ptr, "externalptr")) {
    valid <- FALSE
    msg <- c(msg, "The 'ptr' slot does not contain an external pointer.")
  }

  if (!(object@return_as %in% c(
    "asis", "array", "matrix", "data.frame",
    "data.table", "tibble", "arrow_table", "arrow"
  ))) {
    valid <- FALSE
    msg <- c(msg, paste(
      "The 'return_as' slot must contain one of 'asis', 'array', 'matrix',",
      "'data.frame', 'data.table', 'tibble', 'arrow_table' or 'arrow'."
    ))
  }

  if (!is.logical(object@query_statistics)) {
    valid <- FALSE
    msg <- c(msg, "The 'query_statistics' slot does not contain a logical value.")
  }

  if (!is.logical(object@strings_as_factors)) {
    valid <- FALSE
    msg <- c(msg, "The 'strings_as_factors' slot does not contain a logical value.")
  }

  if (!is.logical(object@keep_open)) {
    valid <- FALSE
    msg <- c(msg, "The 'keep_open' slot does not contain a logical value.")
  }

  if (valid) TRUE else msg
})


## Internal helper function to map DATETIME_* data to the internal representation (where
## we mostly follow NumPy). An example is DATETIME_YEAR where the current year (2021) is
## encoded as the offset relative to the _year_ of the epoch, i.e. 51.  When an R user submits
## a date type as a min or max value for a range, if would likely be as.Date("2021-01-01")
## which, being an R date, has an internal representation of _days_ since the epoch, i.e.
## as.numeric(as.Date("2021-01-01")) yields 18628.
##
## We also convert the value to integer64 because that is the internal storage format
.map2integer64 <- function(val, dtype) {
  ## in case it is not a (datetime or (u)int64) type), or already an int64, return unchanged
  if ((!grepl("^DATETIME_", dtype) && !grepl("INT64$", dtype)) || inherits(val, "integer64")) {
    return(val)
  }

  val <- switch(dtype,
    "DATETIME_YEAR" = as.numeric(strftime(val, "%Y")) - 1970,
    "DATETIME_MONTH" = 12 * (as.numeric(strftime(val, "%Y")) - 1970) + as.numeric(strftime(val, "%m")) - 1,
    "DATETIME_WEEK" = as.numeric(val) / 7,
    "DATETIME_DAY" = as.numeric(val),
    "DATETIME_HR" = as.numeric(val) / 3600,
    "DATETIME_MIN" = as.numeric(val) / 60,
    "DATETIME_SEC" = as.numeric(val),
    "DATETIME_MS" = as.numeric(val) * 1e3,
    "DATETIME_US" = as.numeric(val) * 1e6,
    "DATETIME_NS" = as.numeric(val),
    "DATETIME_PS" = as.numeric(val) * 1e3,
    "DATETIME_FS" = as.numeric(val) * 1e6,
    "DATETIME_AS" = as.numeric(val) * 1e9,
    "UINT64" = val,
    "INT64" = val
  )
  bit64::as.integer64(val)
}

#' Returns a TileDB array, allowing for specific subset ranges.
#'
#' Heterogenous domains are supported, including timestamps and characters.
#'
#' This function may still change; the current implementation should be
#' considered as an initial draft.
#' @param x A `tiledb_array` object.
#' @param i optional row index expression which can be a list in which case
#' minimum and maximum of each list element determine a range; multiple list
#' elements can be used to supply multiple ranges.
#' @param j optional column index expression which can be a list in which case
#' minimum and maximum of each list element determine a range; multiple list
#' elements can be used to supply multiple ranges.
#' @param ... Extra parameters for method signature, currently unused.
#' @param drop Optional logical switch to drop dimensions, default FALSE,
#' currently unused.
#' @return The resulting elements in the selected format
#' @import nanotime
#' @importFrom nanoarrow as_nanoarrow_array
#' @aliases [,tiledb_array
#' @aliases [,tiledb_array-method
#' @aliases [,tiledb_array,ANY,tiledb_array-method
#' @aliases [,tiledb_array,ANY,ANY,tiledb_array-method
setMethod(
  "[",
  "tiledb_array",
  function(x, i, j, ..., drop = FALSE) {
    ## add defaults
    if (missing(i)) i <- NULL
    if (missing(j)) j <- NULL
    k <- NULL
    # verbose <- getOption("verbose", FALSE)

    spdl::trace("[tiledb_array] '[' accessor started")

    ## 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() or selected_points().")
    }

    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)

    if (x@return_as == "arrow_table") {
      x@return_as <- "arrow"
    } # normalize

    if (x@return_as %in% c("data.table", "tibble", "arrow")) {
      if (!requireNamespace(x@return_as, quietly = TRUE)) {
        stop("The 'return_as' argument value '", x@return_as, "' requires the package '",
          x@return_as, "' to be installed.",
          call. = FALSE
        )
      }
    }

    use_arrow <- x@return_as == "arrow"
    if (use_arrow) {
      suppressMessages(do.call(rawToChar(as.raw(c(0x72, 0x65, 0x71, 0x75, 0x69, 0x72, 0x65))), list("nanoarrow")))
    }

    dims <- tiledb::dimensions(dom)
    ndims <- length(dims)
    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)
    dimdictionary <- 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)))
    attrdictionary <- unname(sapply(attrs, function(a) libtiledb_attribute_has_enumeration(ctx@ptr, 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()
      attrdictionary <- 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]
      attrdictionary <- attrdictionary[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)
      alldictionary <- c(dimdictionary, attrdictionary)
    } else { # otherwise only return attributes
      allnames <- attrnames
      alltypes <- attrtypes
      allvarnum <- attrvarnum
      allnullable <- attrnullable
      alldictionary <- attrdictionary
    }

    ## 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("['['] memory budget is {}", memory_budget)

    if (length(enckey) > 0) {
      arrptr <- libtiledb_array_open_with_key(ctx@ptr, uri, "READ", enckey)
    } else {
      arrptr <- libtiledb_array_open(ctx@ptr, uri, "READ")
    }
    if (length(x@timestamp_start) > 0) {
      spdl::debug("['['] set open_timestamp_start to {}", x@timestamp_start)
      arrptr <- libtiledb_array_set_open_timestamp_start(arrptr, x@timestamp_start)
    }
    if (length(x@timestamp_end) > 0) {
      spdl::debug("['['] set open_timestamp_end to {}", x@timestamp_end)
      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)
    }

    ## dictionaries are schema-level objects to fetch them now where we expect to have some
    dictionaries <- vector(mode = "list", length = length(allnames))
    names(dictionaries) <- allnames
    ordered_dict <- dictionaries
    for (ii in seq_along(dictionaries)) {
      if (isTRUE(alldictionary[ii])) {
        attr <- attrs[[allnames[ii]]]
        tpstr <- tiledb_attribute_get_enumeration_type_ptr(attr, arrptr)
        if (tpstr %in% c("ASCII", "UTF8")) {
          dictionaries[[ii]] <- tiledb_attribute_get_enumeration_ptr(attr, arrptr)
        } else if (tpstr %in% c(
          "FLOAT32", "FLOAT64", "BOOL",
          "UINT8", "UINT16", "UINT32", "UINT64",
          "INT8", "INT16", "INT32", "INT64"
        )) {
          dictionaries[[ii]] <- tiledb_attribute_get_enumeration_vector_ptr(attr, arrptr)
        } else {
          stop("Unsupported enumeration vector payload of type '%s'", tpstr, call. = FALSE)
        }
        ordered_dict[[ii]] <- tiledb_attribute_is_ordered_enumeration_ptr(attr, arrptr)
        attr(dictionaries[[ii]], "ordered") <- ordered_dict[[ii]]
      }
    }

    ## helper function to sweep over names and types of domain
    getDomain <- function(nm, tp) {
      if (tp %in% c("ASCII", "CHAR", "UTF8")) {
        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)
    }

    ## ensure selected_points, if submitted, is of correct length
    if (length(x@selected_points) != 0 &&
      length(x@selected_points) != length(dimnames) &&
      is.null(names(x@selected_points))) {
      stop(paste0(
        "If points 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
    }

    ## expand a shorter-but-named selected_points list
    if ((length(x@selected_points) < length(dimnames)) &&
      (!is.null(names(x@selected_points)))) {
      fulllist <- vector(mode = "list", length = length(dimnames))
      ind <- match(names(x@selected_points), dimnames)
      if (any(is.na(ind))) stop("Name for selected points does not match dimension names.")
      for (ii in seq_len(length(ind))) {
        fulllist[[ind[ii]]] <- x@selected_points[[ii]]
      }
      x@selected_points <- 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]
    }

    ## selected_points may be in different order than dimnames, so reorder if need be
    if ((length(x@selected_points) == length(dimnames)) &&
      (!is.null(names(x@selected_points))) &&
      (!identical(names(x@selected_points), dimnames))) {
      x@selected_points <- x@selected_points[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 selected_points is still an empty list, make it an explicit one
    if (length(x@selected_points) == 0) {
      x@selected_points <- 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 (ndims == 1) {
        stop("Setting dimension 'j' requires at least two dimensions.", call. = FALSE)
      }
      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 (ndims <= 2) {
        stop("Setting dimension 'k' requires at least three dimensions.", call. = FALSE)
      }
      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@selected_ranges

    ## pointer to subarray needed for iterated setting of points from selected_ranges
    ## and selected_points across all possible dimensions
    have_made_selection <- FALSE
    sbrptr <- libtiledb_subarray(qryptr)

    ## if ranges selected, use those
    for (k in seq_len(length(x@selected_ranges))) {
      if (is.null(x@selected_ranges[[k]]) && is.null(x@selected_points[[k]])) {
        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 - 1, dimtypes[k], vec[1], vec[2])
          spdl::debug("[tiledb_array] Adding non-zero dim {}:{} on {} with ({},{})", k, i, dimtypes[k], vec[1], vec[2])
          rangeunset <- FALSE
          have_made_selection <- TRUE
        }
      } else if (is.null(nrow(x@selected_ranges[[k]])) && is.null(x@selected_points[[k]])) {
        vec <- x@selected_ranges[[k]]
        vec <- .map2integer64(vec, dimtypes[k])
        sbrptr <- libtiledb_subarray_add_range_with_type(sbrptr, k - 1, dimtypes[k], min(vec), max(vec))
        spdl::debug("[tiledb_array] Adding non-zero dim {}:{} on {} with ({},{})", k, i, dimtypes[k], vec[1], vec[2])
        rangeunset <- FALSE
        have_made_selection <- TRUE
      } else if (is.null(x@selected_points[[k]])) {
        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 - 1, dimtypes[k], vec[1], vec[2])
          spdl::debug("[tiledb_array] Adding non-zero dim {}:{} on {} with ({},{})", k, i, dimtypes[k], vec[1], vec[2])
        }
        rangeunset <- FALSE
        have_made_selection <- TRUE
      }
    }

    ## if points selected, use those (and fewer special cases as A[i,j,k] not folded into points)
    for (k in seq_len(length(x@selected_points))) {
      if (!is.null(x@selected_points[[k]])) {
        m <- x@selected_points[[k]]
        for (i in seq_along(m)) {
          vec <- .map2integer64(c(m[i], m[i]), dimtypes[k])
          sbrptr <- libtiledb_subarray_add_range_with_type(sbrptr, k - 1, dimtypes[k], vec[1], vec[2])
          spdl::debug("[tiledb_array] Adding point on non-zero dim {}:{} on {} with ({},{})", k, i, dimtypes[k], vec[1], vec[2])
        }
        rangeunset <- FALSE
        have_made_selection <- TRUE
      }
    }

    if (have_made_selection) {
      libtiledb_query_set_subarray_object(qryptr, sbrptr)
    }

    buflist <- vector(mode = "list", length = length(allnames))

    if (length(x@buffers) != 0) { # if we were given buffers (as in the case of TileDB Cloud ops)
      nm <- names(x@buffers)
      if (!isTRUE(all.equal(nm, allnames))) {
        stop("Expected ", paste(allnames, collapse = ","), " got ", paste(nm, collapse = ","), call. = FALSE)
      }
      for (i in seq_along(allnames)) {
        n <- allnames[i]
        path <- x@buffers[[n]]
        if (!file.exists(path)) stop("No buffer for ", n, call. = FALSE)
        if (is.na(allvarnum[i])) {
          buflist[[i]] <- vlcbuf_from_shmem(path, alltypes[i])
        } else {
          buflist[[i]] <- querybuf_from_shmem(path, alltypes[i])
        }
      }

      ## get results (shmem variant)
      getResultShmem <- function(buf, name, varnum) { # , resrv, qryptr) {
        if (is.na(varnum)) {
          vec <- length_from_vlcbuf(buf)
          libtiledb_query_get_buffer_var_char(buf, vec[1], vec[2])[, 1]
        } else {
          col <- libtiledb_query_get_buffer_ptr(buf, asint64)
          if (!is.null(dictionaries[[name]])) { # if there is a dictionary
            dct <- dictionaries[[name]] # access it from utility
            ord <- ordered_dict[[name]]
            ## the following expands out to a char vector first; we can do better
            ##   col <- factor(dct[col+1], levels=dct)
            ## so we do it "by hand"
            col <- col + 1L # adjust for zero-index C/C++ layer
            attr(col, "levels") <- dct
            attr(col, "class") <- if (ord) c("ordered", "factor") else "factor"
          }
          col
        }
      }
      reslist <- mapply(getResultShmem, buflist, allnames, allvarnum, SIMPLIFY = FALSE)
      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)
      colnames(res) <- allnames
    } else { # -- start 'big else' of standard query build

      ## 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]
          spdl::debug("[getEstimatedSize] column '{}' (is.na(varnum) and !nullable) {}", name, res)
        } else if (is.na(varnum) && nullable) {
          res <- libtiledb_query_get_est_result_size_var_nullable(qryptr, name)[1]
          spdl::debug("[getEstimatedSize] column '{}' (is.na(varnum) and nullable) {}", name, res)
        } else if (!is.na(varnum) && !nullable) {
          res <- libtiledb_query_get_est_result_size(qryptr, name)
          spdl::debug("[getEstimatedSize] column '{}' (!is.na(varnum) and !nullable) {}", name, res)
        } else if (!is.na(varnum) && nullable) {
          res <- libtiledb_query_get_est_result_size_nullable(qryptr, name)[1]
          spdl::debug("[getEstimatedSize] column '{}' (!is.na(varnum) and nullable) {}", name, res)
        }
        if (rangeunset) {
          sz <- tiledb_datatype_string_to_sizeof(datatype)
          res <- res / sz
          spdl::debug("[getEstimatedSize] column '{}' rangeunset and res scaled to {}", name, res)
        }
        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
      spdl::debug("['['] result of size estimates is {}", paste(ressizes, collapse=","))
      idx <- ressizes > 0
      ressizes <- if (any(idx)) {
        ressizes[idx]
      } else {
        0
      }
      resrv <- max(1, min(memory_budget/8, ressizes))
      spdl::debug("['['] overall estimate {} rows", resrv)


      ## allocate and set buffers
      if (!use_arrow) {
        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)
              buf <- libtiledb_query_buffer_var_char_legacy_validity_mode(ctx@ptr, buf)
              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
        )
        spdl::debug("['['] buffers allocated in list")
      }

      ## if we have a query condition, apply it
      if (isTRUE(x@query_condition@init)) {
        qryptr <- libtiledb_query_set_condition(qryptr, x@query_condition@ptr)
      }

      overallresults <- list()
      counter <- 1L
      finished <- FALSE
      while (!finished) {
        if (use_arrow) {
          abptr <- libtiledb_allocate_column_buffers(ctx@ptr, qryptr, uri, allnames, memory_budget)
          spdl::debug("['['] buffers allocated and set")
        }

        ## fire off query
        spdl::debug(
          "['['] query submission: {} array_open {}", counter,
          if (libtiledb_array_is_open(arrptr)) "true" else "false"
        )
        qryptr <- libtiledb_query_submit(qryptr)

        ## check status
        status <- libtiledb_query_status(qryptr)
        # if (status != "COMPLETE") warning("Query returned '", status, "'.", call. = FALSE)
        if (status != "COMPLETE") spdl::debug("['['] query returned '{}'.", status)

        if (use_arrow) {
          ## rl <- libtiledb_to_arrow(abptr, qryptr, dictionaries)
          ## at <- .as_arrow_table(rl)
          na <- libtiledb_to_arrow(abptr, qryptr, dictionaries)
          at <- arrow::as_arrow_table(na)

          ## special case from schema evolution could have added twice so correcting
          for (n in colnames(at)) {
            v <- at[[n]]$as_vector()
            lvls <- levels(v)
            if (inherits(v, "factor")) {
              vec <- as.integer(v)
              vec[vec == -.Machine$integer.max] <- NA_integer_
              if (min(vec, na.rm = TRUE) == 2 && max(vec, na.rm = TRUE) == length(lvls) + 1) {
                vec <- vec - 1L
                attr(vec, "levels") <- attr(v, "levels")
                class(vec) <- class(v)
                at[[n]] <- vec
              }
            }
          }

          ## if dictionaries are to be injected at the R level, this does it
          # for (n in names(dictionaries)) {
          #    if (!is.null(dictionaries[[n]])) {
          #        at[[n]] <- arrow::DictionaryArray$create(at[[n]]$as_vector(), dictionaries[[n]])
          #    }
          # }
          overallresults[[counter]] <- at
          spdl::debug("['['] received arrow table {}", counter)
        }

        ## close array
        if (status == "COMPLETE") {
          if (!x@keep_open) libtiledb_array_close(arrptr)
          .pkgenv[["query_status"]] <- status
          finished <- TRUE
        }

        if (!use_arrow) {
          ## retrieve actual result size (from fixed size element columns)
          getResultSize <- function(name, varnum, qryptr) {
            val <- 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)
            }
            spdl::debug("[getResultSize] name {} varnum {} has {}", name, varnum, val)
            val
          }
          estsz <- mapply(getResultSize, allnames, allvarnum, MoreArgs = list(qryptr = qryptr), SIMPLIFY = TRUE)
          spdl::debug("['['] 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("['['] expected size {}", resrv)
          ## Permit one pass to allow zero-row schema read
          if (resrv == 0 && counter > 1L) {
            finished <- TRUE
            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
            ## message("For ", name, " seeing ", estsz, " and ", varnum)
            spdl::debug("[getResult] name {} estsz {} varnum {}", name, estsz, varnum)
            if (is.na(varnum)) {
              spdl::debug("[getResult] varnum before libtiledb_query_result_buffer_elements_vec")
              vec <- libtiledb_query_result_buffer_elements_vec(qryptr, name)
              if (has_dumpbuffers) {
                vlcbuf_to_shmem(x@dumpbuffers, name, buf, vec)
              }
              spdl::debug("[getResult] varnum before libtiledb_query_get_buffer_var_char")
              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)]
              spdl::debug("[getResult] calling libtiledb_query_get_buffer_ptr")
              col <- libtiledb_query_get_buffer_ptr(buf, asint64)[seq_len(estsz)]
              if (!is.null(dictionaries[[name]])) { # if there is a dictionary
                dct <- dictionaries[[name]] # access it from utility
                ord <- ordered_dict[[name]]

                col <- col + 1L # adjust for zero-index C/C++ layer

                if (inherits(col, "integer64")) { # can happen when Python writes
                  col <- as.integer(col)
                }

                ## special case from schema evolution could have added twice so correct
                if (length(col) > 0 && min(col, na.rm = TRUE) == 2 && max(col, na.rm = TRUE) == length(dct) + 1) {
                  col <- col - 1L
                }

                if (inherits(dct, "character")) {
                  attr(col, "levels") <- dct
                  attr(col, "class") <- if (ord) c("ordered", "factor") else "factor"
                } else {
                  col <- dct[col]
                }
              }
              col
            }
          }
          spdl::debug("['['] getting results")
          reslist <- mapply(getResult, buflist, allnames, allvarnum, estsz,
            MoreArgs = list(qryptr = qryptr), SIMPLIFY = FALSE
          )
          spdl::debug("['['] got results")
          ## 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))))
            }
          }
          ## the list columns are now all of equal lenthth as R needs and we can form a data.frame
          res <- data.frame(reslist)[, , drop = FALSE]
          colnames(res) <- allnames
          overallresults[[counter]] <- res
        }
        spdl::debug("['['] completed {}", counter)
        counter <- counter + 1L
      }

      if (!use_arrow && requireNamespace("data.table", quietly = TRUE)) { # use very efficient rbindlist if available
        res <- as.data.frame(data.table::rbindlist(overallresults))
      } else {
        res <- do.call(rbind, overallresults)
      }
      spdl::debug("['['] returning 'res'")
      res
    } # end of 'big else' for query build, submission and read

    if (!use_arrow) {
      ## convert to factor if that was asked
      if (x@strings_as_factors) {
        for (n in colnames(res)) {
          if (is.character(res[[n]])) {
            res[[n]] <- as.factor(res[[n]])
          }
        }
      }

      ## reduce output if extended is false, or attrs given
      if (!x@extended) {
        if (length(sel) > 0) {
          res <- res[, if (sparse) allnames else attrnames, drop = FALSE]
        }
        k <- match("__tiledb_rows", colnames(res))
        if (is.finite(k)) {
          res <- res[, -k, drop = FALSE]
        }
      }
    }

    spdl::debug("['['] before preparing final data form")
    if (x@return_as == "asis") {
      spdl::debug("['['] return asis")
      res <- as.list(res)
    } else if (x@return_as == "array") { # if a conversion preference has been given, use it
      res <- .convertToArray(dimnames, attrnames, res)
    } else if (x@return_as == "matrix") {
      res <- .convertToMatrix(res)
    } else if (x@return_as == "data.frame") {
      res <- as.data.frame(res) # should already be one per above
    } else if (x@return_as == "data.table" && requireNamespace("data.table", quietly = TRUE)) {
      res <- data.table::data.table(res)
    } else if (x@return_as == "tibble" && requireNamespace("tibble", quietly = TRUE)) {
      res <- tibble::as_tibble(res)
    } else if (use_arrow) {
      ## possible list already collapsed above
      res
    }

    spdl::debug("['['] getting query status")
    attr(res, "query_status") <- .pkgenv[["query_status"]]
    if (x@query_statistics) {
      attr(res, "query_statistics") <- libtiledb_query_stats(qryptr)
    }

    spdl::debug("['['] returning result")
    invisible(res)
  }
)

## helper functions
.convertToMatrix <- function(res) {
  ## special case of row and colnames and one attribute
  if (typeof(res[, 1]) == "character" && typeof(res[, 2]) == "character" && ncol(res) == 3) {
    dimnames <- list(unique(res[, 1]), unique(res[, 2]))
    res <- matrix(res[, 3], length(dimnames[[1]]), length(dimnames[[2]]),
      dimnames = dimnames, byrow = TRUE
    )
    return(invisible(res))
  }
  k <- match("__tiledb_rows", colnames(res))
  if (is.finite(k)) {
    res <- res[, -k]
  }
  if (ncol(res) < 3) {
    stop("Seeing as.matrix argument with insufficient result set")
  }
  ## special case of integer64
  if (inherits(res[, 1], "integer64")) {
    res[, 1] <- as.integer(res[, 1])
    if (min(res[, 1]) == 0) res[, 1] <- res[, 1] + 1
  }
  if (ncol(res) >= 3 && inherits(res[, 2], "integer64")) {
    res[, 2] <- as.integer(res[, 2])
    if (min(res[, 2]) == 0) res[, 2] <- res[, 2] + 1
  }
  if (!identical(unique(res[, 1]), seq(1, length(unique(res[, 1]))))) {
    cur <- unique(res[, 1])
    for (l in seq_len(length(cur))) res[which(res[, 1] == cur[l]), 1] <- l
  }
  if (!identical(unique(res[, 2]), seq(1, length(unique(res[, 2]))))) {
    cur <- unique(res[, 2])
    for (l in seq_len(length(cur))) res[which(res[, 2] == cur[l]), 2] <- l
  }
  if (ncol(res) == 3) {
    mat <- matrix(, nrow = max(res[, 1]), ncol = max(res[, 2]))
    mat[cbind(res[, 1], res[, 2])] <- res[, 3]
    res <- mat
  } else { # case of ncol > 3
    k <- ncol(res) - 2
    lst <- vector(mode = "list", length = k)
    for (i in seq_len(k)) {
      mat <- matrix(, nrow = max(res[, 1]), ncol = max(res[, 2]))
      mat[cbind(res[, 1], res[, 2])] <- res[, 2 + i]
      lst[[i]] <- mat
    }
    names(lst) <- tail(colnames(res), k)
    res <- lst
  }
  res
}

.convertToArray <- function(dimnames, attrnames, res) {
  dims <- sapply(dimnames, function(n) length(unique(res[, n])), USE.NAMES = FALSE)
  if (prod(dims) != nrow(res)) {
    message("Total array dimensions from unique elements does not match rows, returning data.frame unchanged.")
    return(invisible(res))
  }
  lst <- lapply(attrnames, function(n) array(res[, n], dim = dims))
  names(lst) <- attrnames
  lst
}

#' Sets a tiledb array value or value range
#'
#' This function assigns a right-hand side object, typically a data.frame or
#' something that can be coerced to a data.frame, to a tiledb array.
#'
#' For sparse matrices, row and column indices can either be supplied
#' as part of the left-hand side object, or as part of the data.frame
#' provided appropriate column names.
#'
#' This function may still change; the current implementation should be
#' considered as an initial draft.
#' @param x sparse or dense TileDB array object
#' @param i parameter row index
#' @param j parameter column index
#' @param ... Extra parameter for method signature, currently unused.
#' @param value The value being assigned
#' @return The modified object
#' @examples
#' \dontshow{
#' ctx <- tiledb_ctx(limitTileDBCores())
#' }
#' \dontrun{
#' uri <- "quickstart_sparse" ## as created by the other example
#' arr <- tiledb_array(uri) ## open array
#' df <- arr[] ## read current content
#' ## First approach: matching data.frame with appriate row and column
#' newdf <- data.frame(rows = c(1, 2, 2), cols = c(1, 3, 4), a = df$a + 100)
#' ## Second approach: supply indices explicitly
#' arr[c(1, 2), c(1, 3)] <- c(42, 43) ## two values
#' arr[2, 4] <- 88 ## or just one
#' }
#' @aliases [<-,tiledb_array
#' @aliases [<-,tiledb_array-method
#' @aliases [<-,tiledb_array,ANY,tiledb_array-method
#' @aliases [<-,tiledb_array,ANY,ANY,tiledb_array-method
setMethod(
  "[<-",
  "tiledb_array",
  function(x, i, j, ..., value) {
    if (!is.data.frame(value) && !(is.list(value) && length(value) > 1)) {
      value <- as.data.frame(value)
      if (nrow(value) == 0) {
        message("Cannot assign zero row objects to TileDB Array.")
        return(x)
      }
    }
    if (is.null(names(value))) stop("No column names supplied", call. = FALSE)

    ## add defaults
    if (missing(i)) i <- NULL
    if (missing(j)) j <- NULL
    spdl::debug("[tiledb_array] '[<-' accessor started")

    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)
    ndims <- length(dims)
    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)
    dimdictionary <- 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)))
    attrdictionary <- unname(sapply(attrs, function(a) libtiledb_attribute_has_enumeration(ctx@ptr, a@ptr)))

    if (length(attrnames) > 0) {
      allnames <- c(dimnames, attrnames)
      alltypes <- c(dimtypes, attrtypes)
      allvarnum <- c(dimvarnum, attrvarnum)
      allnullable <- c(dimnullable, attrnullable)
      alldictionary <- c(dimdictionary, attrdictionary)
    } else {
      allnames <- dimnames
      alltypes <- dimtypes
      allvarnum <- dimvarnum
      allnullable <- dimnullable
      alldictionary <- dimdictionary
    }

    ## check we have complete columns (as we cannot write subset of attributes)
    missing_names <- setdiff(attrnames, names(value))
    if (sparse &&
      length(missing_names) > 0 &&
      names(value)[1] != "value") { # special case of unnamed vector 'value' becoming one-col df
      stop("Columns '", paste(missing_names, collapse = ", "), "' are missing. Please add them", call. = FALSE)
    }

    ## we will recognize two standard cases
    ##  1) arr[]    <- value    where value contains two columns with the dimnames
    ##  2) arr[i,j] <- value    where value contains just the attribute names
    ## There is more to do here but it is a start

    ## Case 1
    if (length(colnames(value)) == length(allnames)) {
      ## same length is good
      if (length(intersect(colnames(value), allnames)) == length(allnames)) {
        ## all good, proceed
        # message("Yay all columns found")
        value <- value[, allnames, drop = FALSE] # reordering helps with append case
      } else {
        stop("Assigned data.frame does not contain all required attribute and dimension columns.")
      }
    }

    ## Case 2
    if (sparse && length(colnames(value)) == length(attrnames)) { # FIXME: need to check for array or matrix arg?
      if (is.null(i)) stop("For arrays a row index has to be supplied.")
      if (is.null(j)) stop("For arrays a column index has to be supplied.")
      # if (length(i) != nrow(value)) stop("Row index must have same number of observations as data")
      if (length(j) == 1) j <- rep(j, nrow(value))
      ## if (length(colnames(value)) == 1 && colnames(value) == "value") colnames(value) <- attrnames
      colnames(value) <- attrnames
      newvalue <- data.frame(i, j)
      colnames(newvalue) <- dimnames
      value <- cbind(newvalue, value)
    }

    ## Case 3: dense, length attributes == 1, i and j NULL
    ##         e.g. the quickstart_dense example where the RHS may be a matrix or data.frame
    ##         also need to guard against data.frame object which already have 'rows' and 'cols'
    if (isFALSE(sparse) &&
      ## is.null(i) && is.null(j) &&
      length(attrnames) == 1) {
      d <- dim(value)
      if ((d[2] > 1) &&
        (inherits(value, "data.frame") || inherits(value, "matrix")) &&
        !any(grepl("rows", colnames(value))) &&
        !any(grepl("cols", colnames(value)))) {
        ## turn the 2-d RHS in 1-d and align the names for the test that follows
        ## in effect, we just rewrite the query for the user
        value <- data.frame(x = as.matrix(value)[seq(1, d[1] * d[2])])
        colnames(value) <- attrnames
        allnames <- attrnames
        alltypes <- attrtypes
        allnullable <- attrnullable
        alldictionary <- attrdictionary
      }

      ## Case 4: dense, list on RHS e.g. the ex_1.R example
    } else if (isFALSE(sparse) &&
      ## is.null(i) && is.null(j) &&
      length(value) == length(attrnames)) {
      if (!inherits(value, "data.frame")) {
        nl <- length(value)
        for (k in seq_len(nl)) {
          d <- dim(value[[k]])
          value[[k]] <- as.matrix(value[[k]])[seq(1, prod(d))]
        }
      }
      names(value) <- attrnames
      allnames <- attrnames
      alltypes <- attrtypes
      allnullable <- attrnullable
      alldictionary <- attrdictionary
    }

    nc <- if (is.list(value)) length(value) else ncol(value)
    nm <- if (is.list(value)) names(value) else colnames(value)

    if (isTRUE(all.equal(sort(allnames), sort(nm)))) {
      if (libtiledb_array_is_open_for_writing(x@ptr)) { # if open for writing
        arrptr <- x@ptr #   use array
      } else { # else open appropriately
        if (length(enckey) > 0) {
          if (length(tstamp) > 0) {
            arrptr <- libtiledb_array_open_at_with_key(ctx@ptr, uri, "WRITE", enckey, tstamp)
          } else {
            arrptr <- libtiledb_array_open_with_key(ctx@ptr, uri, "WRITE", enckey)
          }
        } else {
          if (length(tstamp) > 0) {
            spdl::debug("['[<-'] openning for WRITE at {}", tstamp)
            arrptr <- libtiledb_array_open_at(ctx@ptr, uri, "WRITE", tstamp)
          } else {
            spdl::debug("['[<-'] openning for WRITE")
            arrptr <- libtiledb_array_open(ctx@ptr, uri, "WRITE")
          }
        }
      }

      qryptr <- libtiledb_query(ctx@ptr, arrptr, "WRITE")
      qryptr <- libtiledb_query_set_layout(
        qryptr,
        if (isTRUE(nchar(layout) > 0)) {
          layout
        } else {
          if (sparse) "UNORDERED" else "COL_MAJOR"
        }
      )

      buflist <- vector(mode = "list", length = nc)
      legacy_validity <- libtiledb_query_buffer_var_char_get_legacy_validity_value(ctx@ptr)

      for (colnam in allnames) {
        ## when an index column is use this may be unordered to remap to position in 'nm' names
        k <- match(colnam, nm)

        if (alldictionary[k]) {
          spdl::trace("[tiledb_array] '[<-' column {} ({}) is factor", colnam, k)
          new_levels <- levels(value[[k]])

          attr <- attrs[[allnames[k]]]
          tpstr <- tiledb_attribute_get_enumeration_type_ptr(attr, arrptr)
          if (tpstr %in% c("ASCII", "UTF8")) {
            dictionary <- tiledb_attribute_get_enumeration_ptr(attr, arrptr)
          } else if (tpstr %in% c(
            "FLOAT32", "FLOAT64", "BOOL", "UINT8", "UINT16", "UINT32", "UINT64",
            "INT8", "INT16", "INT32", "INT64"
          )) {
            dictionary <- tiledb_attribute_get_enumeration_vector_ptr(attr, arrptr)
          } else {
            stop("Unsupported enumeration vector payload of type '", tpstr, "'.", call. = FALSE)
          }
          added_enums <- setdiff(new_levels, dictionary)
          if (length(added_enums) > 0) {
            maxval <- tiledb_datatype_max_value(alltypes[k]) + 1 # R vectors are 1-indexed
            spdl::debug(
              "[tiledb_array] '[<-' Adding levels '{}' at '{}' {} ({} + {} ? {})",
              paste(added_enums, collapse = ","), allnames[k], alltypes[k], length(dictionary), length(added_enums), maxval
            )
            if (length(dictionary) + length(added_enums) > maxval) {
              stop(sprintf(
                "For column '%s' cannot add %d factor levels to existing %d for type '%s' with maximum value %d",
                colnam, length(added_enums), length(dictionary), alltypes[k], maxval
              ), call. = FALSE)
            }
            levels <- unique(c(dictionary, new_levels))
            is_ordered <- tiledb_attribute_is_ordered_enumeration_ptr(attr, arrptr)
            value[[k]] <- factor(value[[k]], levels = levels, ordered = is_ordered)
            spdl::trace("[tiledb_array] '[<-' releveled column {} {}", k, is_ordered)
            ase <- tiledb_array_schema_evolution()
            if (!tiledb_array_is_open(x)) {
              arr <- tiledb_array_open(x)
            } else {
              arr <- x
            }
            ase <- tiledb_array_schema_evolution_extend_enumeration(ase, arr, allnames[k], added_enums)
            tiledb::tiledb_array_schema_evolution_array_evolve(ase, uri)
            value[[k]] <- factor(value[[k]], levels = unique(c(dictionary, added_enums)), ordered = is.ordered(value[[k]]))

            } else if (!setequal(new_levels, dictionary) && !is.null(new_levels)) {
            # relevel when having a subset of existing levels, e.g "c" out of c("a","b","c")
            # See issue: https://github.com/TileDB-Inc/TileDB-R/issues/843
            levels <- unique(c(dictionary, new_levels))
            is_ordered <- tiledb_attribute_is_ordered_enumeration_ptr(attr, arrptr)
            value[[k]] <- factor(value[[k]], levels = levels, ordered = is_ordered)
            spdl::trace("[tiledb_array] '[<-' releveled column {} {}", k, is_ordered)
          }
        }

        if (alltypes[k] %in% c("CHAR", "ASCII", "UTF8")) { # variable length
          txtvec <- as.character(value[[k]])
          spdl::debug("[tiledb_array] '[<-' alloc char buffer {} '{}': {}", k, colnam, alltypes[k])
          buflist[[k]] <- libtiledb_query_buffer_var_char_create(txtvec, allnullable[k], legacy_validity)
          qryptr <- libtiledb_query_set_buffer_var_char(qryptr, colnam, buflist[[k]])
        } else {
          col <- value[[k]]
          if (is.list(col)) {
            col <- unname(do.call(c, col))
          }
          if (is.factor(col)) {
            col <- as.integer(col) - 1L # zero based in C++ so offsetting
          }
          nr <- NROW(col)
          spdl::debug("[tiledb_array] '[<-' alloc buf {} '{}': {}, rows: {} null: {} asint64: {}", k, colnam, alltypes[k], nr, allnullable[k], asint64)
          buflist[[k]] <- libtiledb_query_buffer_alloc_ptr(alltypes[k], nr, allnullable[k], allvarnum[k])
          buflist[[k]] <- libtiledb_query_buffer_assign_ptr(buflist[[k]], alltypes[k], col, asint64)
          qryptr <- libtiledb_query_set_buffer_ptr(qryptr, colnam, buflist[[k]])
        }
      }

      ## case of dense array with subarray writes needs to set the subarray
      if (!sparse && !is.null(i) && !is.null(j) && length(allnames) == 1) {
        if (!is.vector(i) || !is.vector(j)) message("'i' and 'j' should be simple vectors.")
        subarr <- as.integer(c(range(i), range(j)))
        qryptr <- libtiledb_query_set_subarray(qryptr, subarr)
      }

      qryptr <- libtiledb_query_submit(qryptr)
      if (!x@keep_open) libtiledb_array_close(arrptr)
    }
    invisible(x)
  }
)

## -- as.data.frame accessor (generic in DenseArray.R)

#' Retrieve data.frame return toggle
#'
#' A \code{tiledb_array} object can be returned as an array (or list of arrays),
#' or, if select, as a \code{data.frame}. This methods returns the
#' selection value.
#' @param object A \code{tiledb_array} object
#' @return A logical value indicating whether \code{data.frame} return
#' is selected
#' @export
setMethod(
  "return.data.frame",
  signature = "tiledb_array",
  function(object) object@as.data.frame
)

## -- as.data.frame setter (generic in DenseArray.R)

#' Set data.frame return toggle
#'
#' A \code{tiledb_array} object can be returned as an array (or list of arrays),
#' or, if select, as a \code{data.frame}. This methods sets the selection value.
#' @param x A \code{tiledb_array} object
#' @param value A logical value with the selection
#' @return The modified \code{tiledb_array} array object
#' @export
setReplaceMethod(
  "return.data.frame",
  signature = "tiledb_array",
  function(x, value) {
    x@as.data.frame <- value
    validObject(x)
    x
  }
)

## -- attrs (generic in Attributes.R and DenseArray.R)

#' Retrieve attributes from \code{tiledb_array} object
#'
#' By default, all attributes will be selected. But if a subset of attribute
#' names is assigned to the internal slot \code{attrs}, then only those
#' attributes#' will be queried.  This methods accesses the slot.
#' @param object A \code{tiledb_array} object
#' @return An empty character vector if no attributes have been selected or else
#' a vector with attributes; \code{NA} means no attributes will be returned.
#' @importFrom methods validObject
#' @export
setMethod(
  "attrs",
  signature = "tiledb_array",
  function(object) object@attrs
)

#' Selects attributes for the given TileDB array
#'
#' @param x A \code{tiledb_array} object
#' @param value A character vector with attributes; the value
#' \code{NA_character_} signals no attributes should be returned; default is an
#' empty character vector implying all columns are returned.
#' @return The modified \code{tiledb_array} object
#' @export
setReplaceMethod(
  "attrs",
  signature = "tiledb_array",
  function(x, value) {
    nm <- names(attrs(schema(x)))
    value_is_na <- length(value) == 1 && is.na(value) # no attribute query
    if (length(nm) == 0 || value_is_na) { # none set so far
      x@attrs <- value
    } else {
      pm <- pmatch(value, nm)
      if (any(is.na(pm))) {
        stop("Multiple partial matches ambiguous: ",
          paste(value[which(is.na(pm))], collapse = ","),
          call. = FALSE
        )
      }
      x@attrs <- nm[pm]
    }
    validObject(x)
    x
  }
)

## -- extended accessor

#' @rdname extended-tiledb_array-method
#' @export
setGeneric("extended", function(object) standardGeneric("extended"))

#' @rdname extended-set-tiledb_array-method
#' @export
setGeneric("extended<-", function(x, value) standardGeneric("extended<-"))

#' Retrieve data.frame extended returns columns toggle
#'
#' A \code{tiledb_array} object can be returned as \code{data.frame}. This
#' methods returns the selection value for \sQuote{extended} format including
#' row  (and column, if present) indices.
#' @param object A \code{tiledb_array} object
#' @return A logical value indicating whether an \code{extended}
#' return is selected
#' @export
setMethod(
  "extended",
  signature = "tiledb_array",
  function(object) object@extended
)

## -- extended setter (generic in DenseArray.R)

#' Set data.frame extended return columns toggle
#'
#' A \code{tiledb_array} object can be returned as \code{data.frame}. This
#' methods set the selection value for \sQuote{extended} format including row
#' (and column, if present) indices.
#' @param x A \code{tiledb_array} object
#' @param value A logical value with the selection
#' @return The modified \code{tiledb_array} array object
#' @export
setReplaceMethod(
  "extended",
  signature = "tiledb_array",
  function(x, value) {
    x@extended <- value
    validObject(x)
    x
  }
)

## -- selected_ranges accessor

#' @rdname selected_ranges-tiledb_array-method
#' @export
setGeneric(
  "selected_ranges",
  function(object) standardGeneric("selected_ranges"))

#' @rdname selected_ranges-set-tiledb_array-method
#' @export
setGeneric(
  "selected_ranges<-",
  function(x, value) standardGeneric("selected_ranges<-"))

#' Retrieve selected_ranges values for the array
#'
#' A \code{tiledb_array} object can have a range selection for each dimension
#' attribute. This methods returns the selection value for
#' \sQuote{selected_ranges} and returns a list (with one element per dimension)
#' of two-column matrices where each row describes one pair of minimum and
#' maximum values. Alternatively, the list can be named with the names providing
#' the match to the corresponding dimension.
#' @param object A \code{tiledb_array} object
#' @return A list which can contain a matrix for each dimension
#' @export
setMethod(
  "selected_ranges",
  signature = "tiledb_array",
  function(object) object@selected_ranges
)

#' Set selected_ranges return values for the array
#'
#' A \code{tiledb_array} object can have a range selection for each dimension
#' attribute. This methods sets the selection value for \sQuote{selected_ranges}
#' which is a list (with one element per dimension) of two-column matrices where
#' each row describes one pair of minimum and maximum values. Alternatively,
#' the list can be named with the names providing the match to the
#' corresponding dimension.
#' @param x A \code{tiledb_array} object
#' @param value A list of two-column matrices where each list element \sQuote{i}
#' corresponds to the dimension attribute \sQuote{i}. The matrices can contain
#' rows where each row contains the minimum and maximum value of a range.
#' @return The modified \code{tiledb_array} array object
#' @export
setReplaceMethod(
  "selected_ranges",
  signature = "tiledb_array",
  function(x, value) {
    x@selected_ranges <- value
    validObject(x)
    x
  }
)

## -- selected_points accessor

#' @rdname selected_points-tiledb_array-method
#' @export
setGeneric(
  "selected_points",
  function(object) standardGeneric("selected_points")
)

#' @rdname selected_points-set-tiledb_array-method
#' @export
setGeneric(
  "selected_points<-",
  function(x, value) standardGeneric("selected_points<-")
)

#' Retrieve selected_points values for the array
#'
#' A \code{tiledb_array} object can have a range selection for each dimension
#' attribute. This methods returns the selection value for
#' \sQuote{selected_points} and returns a list (with one element per dimension)
#' of vectors where each row describes one selected points. Alternatively, the
#' list can be named with the names providing the match to the
#' corresponding dimension.
#' @param object A \code{tiledb_array} object
#' @return A list which can contain a vector for each dimension
#' @export
setMethod(
  "selected_points",
  signature = "tiledb_array",
  function(object) object@selected_points
)

#' Set selected_points return values for the array
#'
#' A \code{tiledb_array} object can have a range selection for each dimension
#' attribute. This methods sets the selection value for \sQuote{selected_points}
#' which is a list (with one element per dimension) of two-column matrices where
#' each row describes one pair of minimum and maximum values. Alternatively, the
#' list can be named with the names providing the match to the
#' corresponding dimension.
#' @param x A \code{tiledb_array} object
#' @param value A list of vectors where each list element \sQuote{i}
#' corresponds to the dimension attribute \sQuote{i}.
#' @return The modified \code{tiledb_array} array object
#' @export
setReplaceMethod(
  "selected_points",
  signature = "tiledb_array",
  function(x, value) {
    x@selected_points <- value
    validObject(x)
    x
  }
)

## -- query_layout accessor

#' @rdname query_layout-tiledb_array-method
#' @export
setGeneric("query_layout", function(object) standardGeneric("query_layout"))

#' @rdname query_layout-set-tiledb_array-method
#' @export
setGeneric(
  "query_layout<-",
  function(x, value) standardGeneric("query_layout<-")
)

#' Retrieve query_layout values for the array
#'
#' A \code{tiledb_array} object can have a corresponding query with a given
#' layout. This method returns the selection value for
#' \sQuote{query_layout} as a character value.
#' @param object A \code{tiledb_array} object
#' @return A character value describing the query layout
#' @export
setMethod("query_layout", signature = "tiledb_array", function(object) object@query_layout)

#' Set query_layout return values for the array
#'
#' A \code{tiledb_array} object can have an associated query with a specific
#' layout. This methods sets the selection value for \sQuote{query_layout}
#' from a  character value.
#' @param x A \code{tiledb_array} object
#'
#' @param value A character variable for the query layout. Permitted values
#' are \dQuote{ROW_MAJOR}, \dQuote{COL_MAJOR}, \dQuote{GLOBAL_ORDER}, or
#' \dQuote{UNORDERED}.
#' @return The modified \code{tiledb_array} array object
#' @export
setReplaceMethod(
  "query_layout",
  signature = "tiledb_array",
  function(x, value) {
    x@query_layout <- value
    validObject(x)
    x
  }
)

## -- datetimes_as_int64 accessor

#' @rdname datetimes_as_int64-tiledb_array-method
#' @export
setGeneric(
  "datetimes_as_int64",
  function(object) standardGeneric("datetimes_as_int64")
)

#' @rdname datetimes_as_int64-set-tiledb_array-method
#' @export
setGeneric(
  "datetimes_as_int64<-",
  function(x, value) standardGeneric("datetimes_as_int64<-")
)

#' Retrieve datetimes_as_int64 toggle
#'
#' A \code{tiledb_array} object may contain date and datetime objects. While
#' their internal representation is generally shielded from the user, it can
#' useful to access them as the \sQuote{native} format which is an
#' \code{integer64}. This function retrieves the current value of the selection
#' variable, which has a default of \code{FALSE}.
#' @param object A \code{tiledb_array} object
#' @return A logical value indicating whether \code{datetimes_as_int64}
#' is selected
#' @export
setMethod(
  "datetimes_as_int64",
  signature = "tiledb_array",
  function(object) object@datetimes_as_int64
)

## -- datetimes_as_int64 setter (generic in DenseArray.R)

#' Set datetimes_as_int64 toggle
#'
#' A \code{tiledb_array} object may contain date and datetime objects. While
#' their internal representation is generally shielded from the user, it can
#' useful to access them as the \sQuote{native} format which is an
#' \code{integer64}. This function set the current value of the selection
#' variable, which has a default of \code{FALSE}.
#' @param x A \code{tiledb_array} object
#' @param value A logical value with the selection
#' @return The modified \code{tiledb_array} array object
#' @export
setReplaceMethod(
  "datetimes_as_int64",
  signature = "tiledb_array",
  function(x, value) {
    x@datetimes_as_int64 <- value
    validObject(x)
    x
  }
)

## -- consolitate wrapper

#' Consolidate fragments of a TileDB Array
#'
#' This function invokes a consolidation operation. Parameters affecting the
#' operation can be set via an optional configuration object. Start and end
#' timestamps can also be set directly.
#' @param uri A character value with the URI of a TileDB Array
#' @param start_time An optional timestamp value, if missing config
#' default is used
#' @param end_time An optional timestamp value, if missing config default is used
#' @param cfg An optional TileDB Configuration object
#' @param ctx An option TileDB Context object
#' @return NULL is returned invisibly
#' @export
array_consolidate <- function(
  uri,
  cfg = NULL,
  start_time,
  end_time,
  ctx = tiledb_get_context()
) {
  stopifnot(`Argument 'uri' must be character` = is.character(uri))
  if (is.null(cfg)) {
    cfg <- config(ctx)
  }

  if (!missing(start_time)) {
    stopifnot(`Argument 'start_time' must be datetime object` = inherits(start_time, "POSIXt"))
    start_time_int64 <- bit64::as.integer64(as.numeric(start_time) * 1000)
    cfg["sm.consolidation.timestamp_start"] <- as.character(start_time_int64)
  }

  if (!missing(end_time)) {
    stopifnot(`Argument 'end_time' must be datetime object` = inherits(end_time, "POSIXt"))
    end_time_int64 <- bit64::as.integer64(as.numeric(end_time) * 1000)
    cfg["sm.consolidation.timestamp_end"] <- as.character(end_time_int64)
  }

  ctx <- tiledb_ctx(cfg)

  libtiledb_array_consolidate(ctx = ctx@ptr, uri = uri, cfgptr = cfg@ptr)
}

#' After consolidation, remove consolidated fragments of a TileDB Array
#'
#' This function can remove fragments following a consolidation step. Note that
#' vacuuming should \emph{not} be run if one intends to use the TileDB
#' \emph{time-traveling} feature of opening arrays at particular timestamps.
#'
#' Parameters affecting the operation can be set via an optional configuration
#' object. Start and end timestamps can also be set directly.
#'
#' @param uri A character value with the URI of a TileDB Array
#' @param start_time An optional timestamp value, if missing config
#' default is used
#' @param end_time An optional timestamp value, if missing config default
#' is used
#' @param cfg An optional TileDB Configuration object
#' @param ctx An option TileDB Context object
#' @return NULL is returned invisibly
#' @export
array_vacuum <- function(
  uri,
  cfg = NULL,
  start_time,
  end_time,
  ctx = tiledb_get_context()
) {
  stopifnot(`Argument 'uri' must be character` = is.character(uri))
  if (is.null(cfg)) {
    cfg <- config(ctx)
  }

  if (!missing(start_time)) {
    stopifnot(`Argument 'start_time' must be datetime object` = inherits(start_time, "POSIXt"))
    start_time_int64 <- bit64::as.integer64(as.numeric(start_time) * 1000)
    cfg["sm.consolidation.timestamp_start"] <- as.character(start_time_int64)
  }

  if (!missing(end_time)) {
    stopifnot(`Argument 'end_time' must be datetime object` = inherits(end_time, "POSIXt"))
    end_time_int64 <- bit64::as.integer64(as.numeric(end_time) * 1000)
    cfg["sm.consolidation.timestamp_end"] <- as.character(end_time_int64)
  }

  ctx <- tiledb_ctx(cfg)

  libtiledb_array_vacuum(ctx = ctx@ptr, uri = uri, cfgptr = cfg@ptr)
}

#' Get the non-empty domain from a TileDB Array by index
#'
#' This functions works for both fixed- and variable-sized dimensions and
#' switches internally.
#'
#' @param arr A TileDB Array
#' @param idx An integer index between one and the number of dimensions
#' @return A two-element object is returned describing the domain of selected
#' dimension; it will either be a numeric vector in case of a fixed-sized
#' dimension or a character vector for a variable-sized one.
#' @export
tiledb_array_get_non_empty_domain_from_index <- function(arr, idx) {
  stopifnot(
    `Argument 'arr' must be a tiledb_array` = is(arr, "tiledb_array"),
    `Argument 'idx' must be numeric and positive` = is.numeric(idx) && idx > 0,
    `Argument 'arr' must be open` = libtiledb_array_is_open(arr@ptr)
  )
  sch <- schema(arr)
  dom <- domain(sch)
  dims <- dimensions(dom)
  dimtypes <- sapply(dims, function(d) libtiledb_dim_get_datatype(d@ptr))
  dimvarnum <- sapply(dims, function(d) libtiledb_dim_get_cell_val_num(d@ptr))

  if (is.na(dimvarnum[idx])) {
    libtiledb_array_get_non_empty_domain_var_from_index(arr@ptr, idx - 1)
  } else {
    libtiledb_array_get_non_empty_domain_from_index(arr@ptr, idx - 1, dimtypes[idx])
  }
}

#' Get the non-empty domain from a TileDB Array by name
#'
#' This functions works for both fixed- and variable-sized dimensions and
#' switches internally.
#'
#' @param arr A TileDB Array
#' @param name An character variable with a dimension name
#' @return A two-element object is returned describing the domain of selected
#' dimension; it will either be a numeric vector in case of a fixed-sized
#' dimension or a character vector for a variable-sized one.
#' @export
tiledb_array_get_non_empty_domain_from_name <- function(arr, name) {
  stopifnot(
    `Argument 'arr' must be a tiledb_array` = is(arr, "tiledb_array"),
    `Argument 'name' must be character` = is.character(name),
    `Argument 'arr' must be open` = libtiledb_array_is_open(arr@ptr)
  )

  sch <- schema(arr)
  dom <- domain(sch)
  dims <- dimensions(dom)
  dimnames <- sapply(dims, function(d) libtiledb_dim_get_name(d@ptr))

  idx <- match(name, dimnames)
  if (is.na(idx)) stop("Argument '", name, "' not among domain names for array.", call. = FALSE)

  tiledb_array_get_non_empty_domain_from_index(arr, idx)
}

## -- matrix return accessors

#' @rdname return.matrix-tiledb_array-method
#' @param ... Currently unused
#' @export
setGeneric(
  "return.matrix",
  function(object, ...) standardGeneric("return.matrix")
)

#' Retrieve matrix return toggle
#'
#' A \code{tiledb_array} object can be returned as an array (or list of arrays),
#' or, if select, as a \code{data.frame} or as a \code{matrix}. This methods
#' returns the selection value for the \code{matrix} selection.
#'
#' @param object A \code{tiledb_array} object
#' @return A logical value indicating whether \code{matrix} return is selected
#' @export
setMethod(
  "return.matrix",
  signature = "tiledb_array",
  function(object) object@as.matrix
)

#' @rdname return.matrix-set-tiledb_array-method
#' @export
setGeneric(
  "return.matrix<-",
  function(x, value) standardGeneric("return.matrix<-")
)

#' Set matrix return toggle
#'
#' A \code{tiledb_array} object can be returned as an array (or list of arrays),
#' or, if select, as a \code{data.frame} or a \code{matrix}. This methods sets
#' the selection value for a \code{matrix}.
#'
#' @param x A \code{tiledb_array} object
#' @param value A logical value with the selection
#' @return The modified \code{tiledb_array} array object
#' @export
setReplaceMethod(
  "return.matrix",
  signature = "tiledb_array",
  function(x, value) {
    x@as.matrix <- value
    validObject(x)
    x
  }
)

## -- query_condition accessors

#' @rdname query_condition-tiledb_array-method
#' @export
setGeneric(
  "query_condition",
  function(object) standardGeneric("query_condition")
)

#' @rdname query_condition-set-tiledb_array-method
#' @export
setGeneric(
  "query_condition<-",
  function(x, value) standardGeneric("query_condition<-")
)

#' Retrieve query_condition value for the array
#'
#' A \code{tiledb_array} object can have a corresponding query condition object.
#' This methods returns it.
#'
#' @param object A \code{tiledb_array} object
#' @return A \code{tiledb_query_condition} object
#' @export
setMethod(
  "query_condition",
  signature = "tiledb_array",
  definition = function(object) object@query_condition
)

#' Set query_condition object for the array
#'
#' A \code{tiledb_array} object can have an associated query condition object to
#' set conditions on the read queries. This methods sets the
#' \sQuote{query_condition} object.
#'
#' @param x A \code{tiledb_array} object
#'
#' @param value A \code{tiledb_query_conditon_object}
#' @return The modified \code{tiledb_array} array object
#' @export
setReplaceMethod(
  "query_condition",
  signature = "tiledb_array",
  function(x, value) {
    stopifnot(`need query_condition object` = is(value, "tiledb_query_condition"))
    x@query_condition <- value
    validObject(x)
    x
  }
)

## -- array return accessors

#' @rdname return.array-tiledb_array-method
#' @param ... Currently unused
#' @export
setGeneric("return.array", function(object, ...) standardGeneric("return.array"))

#' Retrieve array return toggle
#'
#' A \code{tiledb_array} object can be returned as an array (or list of arrays),
#' or, if select, as a \code{data.frame} or as a \code{matrix}. This methods
#' returns the selection value for the \code{array} selection.
#'
#' @param object A \code{tiledb_array} object
#' @return A logical value indicating whether \code{array} return is selected
#' @export
setMethod(
  "return.array",
  signature = "tiledb_array",
  function(object) object@as.array
)

#' @rdname return.array-set-tiledb_array-method
#' @export
setGeneric(
  "return.array<-",
  function(x, value) standardGeneric("return.array<-")
)

#' Set array return toggle
#'
#' A \code{tiledb_array} object can be returned as an array (or list of arrays),
#' or, if select, as a \code{data.frame} or a \code{matrix}. This methods sets
#' the selection value for a \code{array}.
#'
#' @param x A \code{tiledb_array} object
#' @param value A logical value with the selection
#' @return The modified \code{tiledb_array} array object
#' @export
setReplaceMethod(
  "return.array",
  signature = "tiledb_array",
  function(x, value) {
    x@as.array <- value
    validObject(x)
    x
  }
)

## -- return_as conversion preference

#' @rdname return_as-tiledb_array-method
#' @param ... Currently unused
#' @export
setGeneric("return_as", function(object, ...) standardGeneric("return_as"))

#' Retrieve return_as conversion preference
#'
#' A \code{tiledb_array} object can be returned as a \sQuote{list} (default),
#' \sQuote{array}, \sQuote{matrix}, \sQuote{data.frame}, \sQuote{data.table} or
#' \sQuote{tibble}. This method permits to select a preference for the returned
#' object. The default value of \sQuote{asis} means that no conversion
#' is performed.
#'
#' @param object A \code{tiledb_array} object
#' @return A character value indicating the preferred conversion where the value
#' is one of \sQuote{asis} (the default), \sQuote{array},
#' \sQuote{matrix},\sQuote{data.frame}, \sQuote{data.table}, or \sQuote{tibble}.
#' @export
setMethod(
  "return_as",
  signature = "tiledb_array",
  function(object) object@return_as
)

#' @rdname return_as-set-tiledb_array-method
#' @export
setGeneric("return_as<-", function(x, value) standardGeneric("return_as<-"))

#' Retrieve return_as conversion preference
#'
#' A \code{tiledb_array} object can be returned as a \sQuote{list} (default),
#' \sQuote{array}, \sQuote{matrix}, \sQuote{data.frame}, \sQuote{data.table} or
#' \sQuote{tibble}. This method This methods permits to set a preference of
#' returning a \code{list}, \code{array}, \code{matrix}, \code{data.frame}, a
#' \code{data.table}, or a \code{tibble}. The default value of \dQuote{asis}
#' means that no conversion is performed and a \code{list} is returned.
#'
#' @param x A \code{tiledb_array} object
#' @param value A character value with the selection
#' @return The modified \code{tiledb_array} array object
#' @export
setReplaceMethod(
  "return_as",
  signature = "tiledb_array",
  function(x, value) {
    x@return_as <- value
    validObject(x)
    x
  }
)

## -- query_statistics return toggle

#' @rdname query_statistics-tiledb_array-method
#' @param ... Currently unused
#' @export
setGeneric(
  "query_statistics",
  function(object, ...) standardGeneric("query_statistics")
)

#' Retrieve query_statistics toggle
#'
#' A \code{tiledb_array} object can, if requested, return query statistics as a
#' JSON string in an attribute \sQuote{query_statistics} attached to the return
#' object. The default value of the logical switch is \sQuote{FALSE}. This
#' method returns the current value.
#'
#' @param object A \code{tiledb_array} object
#' @return A logical value indicating whether query statistics are returned.
#' @export
setMethod(
  "query_statistics",
  signature = "tiledb_array",
  function(object) object@query_statistics
)

#' @rdname query_statistics-set-tiledb_array-method
#' @export
setGeneric(
  "query_statistics<-",
  function(x, value) standardGeneric("query_statistics<-")
)

#' Set query_statistics toggle
#'
#' A \code{tiledb_array} object can, if requested, return query statistics as a
#' JSON string in an attribute \sQuote{query_statistics} attached to the return
#' object. The default value of the logical switch is \sQuote{FALSE}. This
#' method  sets the value.
#'
#' @param x A \code{tiledb_array} object
#' @param value A logical value with the selection
#' @return The modified \code{tiledb_array} array object
#' @export
setReplaceMethod(
  "query_statistics",
  signature = "tiledb_array",
  function(x, value) {
    x@query_statistics <- value
    validObject(x)
    x
  }
)

## -- strings_as_factors getter/setter

#' @rdname strings_as_factors-tiledb_array-method
#' @export
setGeneric(
  "strings_as_factors",
  function(object) standardGeneric("strings_as_factors")
)

#' @rdname strings_as_factors-set-tiledb_array-method
#' @export
setGeneric(
  "strings_as_factors<-",
  function(x, value) standardGeneric("strings_as_factors<-")
)

#' Retrieve strings_as_factors conversion toggle
#'
#' A \code{tiledb_array} object containing character column can have those
#' converted to factors variables. This methods returns the selection value
#' for \sQuote{strings_as_factors}.
#'
#' @param object A \code{tiledb_array} object
#' @return A logical value indicating whether an \code{strings_as_factors}
#' return is selected
#' @export
setMethod(
  "strings_as_factors",
  signature = "tiledb_array",
  function(object) object@strings_as_factors
)

#' Set strings_as_factors return toggle
#'
#' A \code{tiledb_array} object containing character column can have those
#' converted to factors variables. This methods sets the selection value for
#' \sQuote{strings_as_factors}.
#'
#' @param x A \code{tiledb_array} object
#' @param value A logical value with the selection
#' @return The modified \code{tiledb_array} array object
#' @export
setReplaceMethod(
  "strings_as_factors",
  signature = "tiledb_array",
  function(x, value) {
    x@strings_as_factors <- value
    validObject(x)
    x
  }
)

## piped query support

#' @rdname generics
#' @export
setGeneric("tdb_filter", function(x, ...) standardGeneric("tdb_filter"))

#' Filter from array for query via logical conditions
#'
#' @param x A tiledb_array object as first argument, permitting piping
#' @param ... One or more expressions that are parsed as query_condition objects
#' @param strict A boolean toogle to, if set, errors if a non-existing attribute
#' is selected or filtered on, defaults to 'TRUE'; if 'FALSE' a warning is shown
#' by execution proceeds.
#' @return The tiledb_array object, permitting piping
#' @export
setMethod(
  "tdb_filter",
  signature("tiledb_array"),
  function(x, ..., strict = TRUE) {
    qc <- parse_query_condition(..., ta = x, debug = FALSE, strict = strict)
    if (is.null(qc)) {
      return(x)
    }
    if (isTRUE(x@query_condition@init)) { # if prior qc exists, combine by AND
      x@query_condition <- tiledb_query_condition_combine(x@query_condition, qc, "AND")
    } else { # else just assign
      x@query_condition <- qc
    }
    x
  }
)

#' @rdname generics
#' @export
setGeneric("tdb_select", function(x, ...) standardGeneric("tdb_select"))

#' Select attributes from array for query
#'
#' @param x A tiledb_array object as first argument, permitting piping
#' @param ... One or more attributes of the query
#' @return The tiledb_array object, permitting piping
#' @export
setMethod("tdb_select", signature("tiledb_array"), function(x, ...) {
  if (length(x@sil) == 0) x@sil <- .fill_schema_info_list(x@uri)
  ## helper with a nod to data.table and its name_dots
  names_from_dots <- function(...) {
    dot_sub <- as.list(substitute(list(...)))[-1L]
    vnames <- character(length(dot_sub))
    notnamed <- vnames == ""
    syms <- sapply(dot_sub, is.symbol) # save the deparse() in most cases of plain symbol
    for (i in which(notnamed)) {
      tmp <- if (syms[i]) as.character(dot_sub[[i]]) else deparse(dot_sub[[i]])[1L]
      if (tmp == make.names(tmp)) vnames[i] <- tmp
    }
    vnames
  }

  vec <- names_from_dots(...)
  ind <- match(vec, x@sil$names) # match against schema names
  ind <- ind[x@sil$status[ind] == 2L] # allow only attributes (where status == 2)
  newvec <- na.omit(x@sil$names[ind]) # and create subset (filtering NA for wrong entry)
  x@attrs <- newvec
  x
})

#' @rdname generics
#' @export
setGeneric("tdb_collect", function(x, ...) standardGeneric("tdb_collect"))

#' Collect the query results to finalize piped expression
#'
#' @param x A tiledb_array object as first argument, permitting piping
#' @param ... Ignored
#' @return The object returning from a tiledb_array query (the type of which
#' can be set via the return preference mechanism, see the help for
#' \code{"["} accessor)
#' @export
setMethod("tdb_collect", signature("tiledb_array"), function(x, ...) {
  x[]
})

# unexported helper
.fill_schema_info_list <- function(ta) {
  sch <- schema(ta)
  list(
    names = tiledb_schema_get_names(sch),
    types = tiledb_schema_get_types(sch),
    status = tiledb_schema_get_dim_attr_status(sch),
    enum = tiledb_schema_get_enumeration_status(sch)
  )
}

## Entry points for tiledb_dense and tiledb_sparse

#' @rdname tiledb_array
#' @param ... Used as a pass-through for \code{tiledb_dense}
#' and \code{tiledb_sparse} aliasing
#' @export
tiledb_dense <- function(...) {
  if (isFALSE("tiledb_dense_called" %in% names(.pkgenv))) {
    message(
      "The 'tiledb_dense' function has been removed following a long deprecation. ",
      "This call will be forwarded to 'tiledb_array(..., is.sparse=FALSE)'."
    )
    .pkgenv[["tiledb_dense_called"]] <- TRUE # ensure we nag only once per session
  }
  tiledb_array(..., is.sparse = FALSE)
}

#' @rdname tiledb_array
#' @export
tiledb_sparse <- function(...) {
  if (isFALSE("tiledb_sparse_called" %in% names(.pkgenv))) {
    message(
      "The 'tiledb_sparse' function has been removed following a long deprecation. ",
      "This call will be forwarded to 'tiledb_array(..., is.sparse=TRUE)'."
    )
    .pkgenv[["tiledb_sparse_called"]] <- TRUE # ensure we nag only once per session
  }
  tiledb_array(..., is.sparse = TRUE)
}