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Revisit array opening #279

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Merged
eddelbuettel merged 3 commits into from
Aug 5, 2021
Merged

Revisit array opening #279

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03d4746
refactor array access in [] function
eddelbuettel Jul 23, 2021
de4ec36
when writing, do not reopen if already open for writing
eddelbuettel Aug 5, 2021
18c1d17
have fromDataFrame open for write before writing
eddelbuettel Aug 5, 2021
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2 changes: 1 addition & 1 deletion R/DataFrame.R
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Original file line number Diff line number Diff line change
Expand Up @@ -206,7 +206,7 @@ fromDataFrame <- function(obj, uri, col_index=NULL, sparse=FALSE, allows_dups=sp
allows_dups(schema) <- allows_dups
tiledb_array_create(uri, schema)

df <- tiledb_array(uri)
df <- tiledb_array(uri, query_type = "WRITE")
## when setting an index when likely want 'sparse write to dense array
if (!is.null(col_index) && !sparse) query_layout(df) <- "UNORDERED"
if (is.null(col_index) && sparse)
Expand Down
53 changes: 16 additions & 37 deletions R/TileDBArray.R
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Expand Up @@ -153,6 +153,7 @@ tiledb_array <- function(uri,
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) {
Expand Down Expand Up @@ -431,32 +432,6 @@ setMethod("[", "tiledb_array",

sparse <- libtiledb_array_schema_sparse(sch@ptr)

if (length(enckey) > 0) {
if (length(tstamp) > 0) {
x@ptr <- libtiledb_array_open_at_with_key(ctx@ptr, uri, "READ", enckey, tstamp)
} else {
x@ptr <- libtiledb_array_open_with_key(ctx@ptr, uri, "READ", enckey)
}
} else {
if (length(tstamp) > 0) {
x@ptr <- libtiledb_array_open_at(ctx@ptr, uri, "READ", tstamp)
} else {
x@ptr <- libtiledb_array_open(ctx@ptr, uri, "READ")
}
}

if (length(x@timestamp_start) > 0) {
libtiledb_array_set_open_timestamp_start(x@ptr, x@timestamp_start)
}
if (length(x@timestamp_end) > 0) {
libtiledb_array_set_open_timestamp_end(x@ptr, x@timestamp_end)
}
if (length(x@timestamp_start) > 0 || length(x@timestamp_end) > 0) {
x@ptr <- libtiledb_array_reopen(x@ptr)
}

on.exit(libtiledb_array_close(x@ptr))

dims <- tiledb::dimensions(dom)
dimnames <- sapply(dims, function(d) libtiledb_dim_get_name(d@ptr))
dimtypes <- sapply(dims, function(d) libtiledb_dim_get_datatype(d@ptr))
Expand Down Expand Up @@ -915,20 +890,24 @@ setMethod("[<-", "tiledb_array",

if (all.equal(sort(allnames),sort(nm))) {

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) {
arrptr <- libtiledb_array_open_at(ctx@ptr, uri, "WRITE", tstamp)
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 {
arrptr <- libtiledb_array_open(ctx@ptr, uri, "WRITE")
if (length(tstamp) > 0) {
arrptr <- libtiledb_array_open_at(ctx@ptr, uri, "WRITE", tstamp)
} else {
arrptr <- libtiledb_array_open(ctx@ptr, uri, "WRITE")
}
}
}

}

qryptr <- libtiledb_query(ctx@ptr, arrptr, "WRITE")
qryptr <- libtiledb_query_set_layout(qryptr,
Expand Down