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Support STRING_ASCII attribute columns #276

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Merged
eddelbuettel merged 2 commits into from
Jul 28, 2021
Merged

Support STRING_ASCII attribute columns #276

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0dfaf75
add STRING_ASCII support from data frame and in query condition
eddelbuettel Jul 26, 2021
9f45846
add test
eddelbuettel Jul 27, 2021
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5 changes: 2 additions & 3 deletions R/DataFrame.R
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Original file line number Diff line number Diff line change
Expand Up @@ -177,7 +177,7 @@ fromDataFrame <- function(obj, uri, col_index=NULL, sparse=FALSE, allows_dups=sp
else if (cl == "numeric")
tp <- "FLOAT64"
else if (cl == "character")
tp <- "CHAR"
tp <- "ASCII"
else if (cl == "Date")
tp <- "DATETIME_DAY"
else if (cl == "POSIXct" || cl == "POSIXlt")
Expand All @@ -193,14 +193,13 @@ fromDataFrame <- function(obj, uri, col_index=NULL, sparse=FALSE, allows_dups=sp
}
tiledb_attr(colnames(obj)[ind],
type = tp,
ncells = ifelse(tp=="CHAR",NA_integer_,1),
ncells = ifelse(tp %in% c("CHAR","ASCII"), NA_integer_, 1),
filter_list = filterlist,
nullable = any(is.na(col)))
}
cols <- seq_len(dims[2])
if (!is.null(col_index)) cols <- cols[-col_index]
attributes <- sapply(cols, makeAttr)

schema <- tiledb_array_schema(dom, attrs = attributes,
cell_order = cell_order, tile_order = tile_order,
sparse=sparse, capacity=capacity)
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17 changes: 12 additions & 5 deletions R/QueryCondition.R
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Expand Up @@ -107,7 +107,14 @@ tiledb_query_condition_combine <- function(lhs, rhs, op) {
parse_query_condition <- function(expr, debug=FALSE) {
.isComparisonOperator <- function(x) as.character(x) %in% c(">", ">=", "<", "<=", "==", "!=")
.isBooleanOperator <- function(x) as.character(x) %in% c("&&", "||", "!")
.isAscii <- function(x) grepl("^[a-zA-Z_]*$", x)
.isInteger <- function(x) as.character(as.integer(x)) == x
.isDouble <- function(x) as.character(as.numeric(x)) == x && grepl("[\\.]", as.character(x))
.getType <- function(x) {
if (.isAscii(as.character(x))) "ASCII"
else if (.isDouble(as.character(x))) "FLOAT64"
else "INT32"
}
.mapOpToCharacter <- function(x) switch(x,
`>` = "GT",
`>=` = "GE",
Expand Down Expand Up @@ -135,12 +142,12 @@ parse_query_condition <- function(expr, debug=FALSE) {
} else if (.isComparisonOperator(x[1])) {
if (debug) cat(" [",as.character(x[2]),"] ",
as.character(x[1]), " (aka ", .mapOpToCharacter(as.character(x[1])), ")",
" [",as.character(x[3]), "]",
if (.isInteger(as.character(x[3]))) " int" else " float",
"\n", sep="")
" [",as.character(x[3]), "] ", .getType(x[3]), "\n", sep="")
ch <- as.character(x[3])
dtype <- .getType(ch)
tiledb_query_condition_init(attr = as.character(x[2]), # still need to check again schema
value = as.numeric(as.character(x[3])),
dtype = if (.isInteger(as.character(x[3]))) "INT32" else "FLOAT64",
value = if (dtype == "ASCII") ch else as.numeric(ch),
dtype = dtype,
op = .mapOpToCharacter(as.character(x[1])))
} else {
stop("Unexpected token in expression: ", format(x))
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20 changes: 19 additions & 1 deletion inst/tinytest/test_querycondition.R
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Expand Up @@ -94,7 +94,7 @@ expect_equal(nrow(ndf), 10)
tiledb_array_close(arr)
rm(qry)

## check b == 115.5 (yes, yes, yes, we know EQ dicey on floats; can remove this if it croaks)
## check b == 115.5 (yes, yes, yes, we know EQ is dicey on floats; can remove this if it croaks)
qry <- tiledb_query(arr, "READ")
rows <- integer(20)
cola <- integer(20)
Expand Down Expand Up @@ -159,6 +159,7 @@ res <- arr2[]
expect_equal(NROW(res), 34L)
expect_true(all(res$bill_length_mm < 40))
expect_true(all(res$year == 2009))

unlink(uri, recursive=TRUE)

## parse query condition support
Expand All @@ -176,3 +177,20 @@ res <- arrwithqc2[]
expect_equal(NROW(res), 34L)
expect_true(all(res$bill_length_mm < 40))
expect_true(all(res$year == 2009))

unlink(uri, recursive=TRUE)

## qc and string_ascii
uri <- tempfile()
fromDataFrame(na.omit(penguins), uri, sparse=TRUE)
qc3 <- parse_query_condition(sex == "male")
arrwithqc3 <- tiledb_array(uri, as.data.frame=TRUE, query_condition=qc3)
res <- arrwithqc3[]
expect_equal(NROW(res), 168L)
expect_true(all(res$sex == "male"))

qc <- tiledb_query_condition_init("sex", "female", "ASCII", "EQ")
arrwithqc <- tiledb_array(uri, as.data.frame=TRUE, query_condition=qc)
res <- arrwithqc[]
expect_equal(NROW(res), 165L)
expect_true(all(res$sex != "male"))
14 changes: 12 additions & 2 deletions src/libtiledb.cpp
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Expand Up @@ -1277,14 +1277,21 @@ XPtr<tiledb::Attribute> libtiledb_attribute(XPtr<tiledb::Context> ctx,
} else if (attr_dtype == TILEDB_FLOAT32) {
using DType = tiledb::impl::tiledb_to_type<TILEDB_FLOAT32>::type;
attr = XPtr<tiledb::Attribute>(new tiledb::Attribute(tiledb::Attribute::create<DType>(*ctx.get(), name)), false);
} else if (attr_dtype == TILEDB_CHAR || attr_dtype == TILEDB_STRING_ASCII) {
} else if (attr_dtype == TILEDB_CHAR) {
using DType = tiledb::impl::tiledb_to_type<TILEDB_CHAR>::type;
attr = XPtr<tiledb::Attribute>(new tiledb::Attribute(tiledb::Attribute::create<DType>(*ctx.get(), name)), false);
uint64_t num = static_cast<uint64_t>(ncells);
if (ncells == R_NaInt) {
num = TILEDB_VAR_NUM; // R's NA is different from TileDB's NA
}
attr->set_cell_val_num(num);
} else if (attr_dtype == TILEDB_STRING_ASCII) {
attr = XPtr<tiledb::Attribute>(new tiledb::Attribute(*ctx.get(), name, TILEDB_STRING_ASCII), false);
uint64_t num = static_cast<uint64_t>(ncells);
if (ncells == R_NaInt) {
num = TILEDB_VAR_NUM; // R's NA is different from TileDB's NA
}
attr->set_cell_val_num(num);
} else if (attr_dtype == TILEDB_DATETIME_YEAR ||
attr_dtype == TILEDB_DATETIME_MONTH ||
attr_dtype == TILEDB_DATETIME_WEEK ||
Expand Down Expand Up @@ -3295,8 +3302,11 @@ void libtiledb_query_condition_init(XPtr<tiledb::QueryCondition> query_cond,
double v = as<double>(condition_value);
uint64_t cond_val_size = sizeof(double);
query_cond->init(attr_name, (void*) &v, cond_val_size, op);
} else if (cond_val_type == "ASCII") {
std::string v = as<std::string>(condition_value);
query_cond->init(attr_name, v, op);
} else {
Rcpp::stop("Currently unsupport type: %s", cond_val_type);
Rcpp::stop("Currently unsupported type: %s", cond_val_type);
}
#endif
}
Expand Down