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Feature/naids #126

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merged 9 commits into from
Aug 22, 2020
Merged

Feature/naids #126

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c2db8f8
Set up new id expectations inc allowing NAs
jefferis Jul 16, 2020
2888bd9
add some tests for valid_id
jefferis Jul 16, 2020
b6abfaf
Pass through NAs
jefferis Jul 16, 2020
5e32134
make sure to remove NAs from validity tests
jefferis Jul 23, 2020
fb07564
Pass through input consisting only of NAs
jefferis Jul 23, 2020
b9bee24
Treat "" like NA ids
jefferis Jul 23, 2020
3f9641c
Make sure valid_id rejects length 0 inputs
jefferis Jul 23, 2020
64cb73f
neuprint_ids should not treat NA_character as query
jefferis Jul 23, 2020
97cb0cf
Complete basic implementation of NA ids
jefferis Jul 27, 2020
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15 changes: 10 additions & 5 deletions R/ids.R
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Original file line number Diff line number Diff line change
Expand Up @@ -5,13 +5,15 @@ looks_like_bodyid <- function(x) {

# this is more stringent
valid_id <- function(x) {
!isFALSE(tryCatch(id2bit64(x), error=function(e) FALSE))
converted=tryCatch(id2bit64(x), error=function(e) NA)
length(converted)>0 && !any(is.na(converted))
}


# private function to convert 1 or more 64 bit ids (e.g. body ids) to JSON
id2json <- function(x, uniqueids=FALSE, ...) {
bx=id2bit64(x)
if(any(is.na(bx))) stop("cannot reliably JSON encode NA ids!")
if(isTRUE(uniqueids)) bx=unique(bx)
jsonlite::toJSON(bx, ...)
}
Expand All @@ -32,7 +34,7 @@ id2bit64 <- function(x) {
}
if(isTRUE(is.character(x))) {
# bit64::as.integer64("") returns 0 so we need to flag these as NA
x[nchar(x)==0]=NA_character_
x[nchar(x)==0 | is.na(x)]=NA_character_
} else if(bit64::is.integer64(x)) {
# do nothing
} else if(is.integer(x)){
Expand All @@ -43,18 +45,21 @@ id2bit64 <- function(x) {
} else if(is.double(x)) {
# biggest int that can be represented as double 2^(mantissa bits + 1)
BIGGESTFLOAT=2^53+1
if(any(x>BIGGESTFLOAT))
if(any(x>BIGGESTFLOAT, na.rm = TRUE))
stop("Some 64 bit ids cannot be exactly represented as floating point ",
"(double) numbers!\nPlease use character or bit64!")
} else if(is.logical(x) && all(is.na(x))){
# as a special case let these through because NA, a logical value,
# is often used instead of NA_real_, NA_character_ etc
} else {
stop("Unexpected data type for id. Use character, bit64, or numeric!")
}
bx <- bit64::as.integer64(x)
if(any(bx < 0 | is.na(bx)))
if(any(bx < 0, na.rm = TRUE))
stop("Invalid id!")
# unfortunately if we pass a number >9223372036854775807 then we will get
# 9223372036854775807. So we must reject ids >= than this.
if(any(bx>=bit64::as.integer64('9223372036854775807')))
if(any(bx>=bit64::as.integer64('9223372036854775807'), na.rm = TRUE))
stop('I can only cope with ids < 9223372036854775807')
bx
}
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2 changes: 1 addition & 1 deletion R/name.R
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Expand Up @@ -364,7 +364,7 @@ neuprint_search <- function(search, field = "name", fixed=FALSE, exact=NULL,
#' @rdname neuprint_search
#' @importFrom stats na.omit
neuprint_ids <- function(x, mustWork=TRUE, unique=TRUE, fixed=TRUE, conn=NULL, dataset=NULL, ...) {
if(is.character(x) && length(x)==1 && !looks_like_bodyid(x)) {
if(is.character(x) && length(x)==1 && !looks_like_bodyid(x) && !is.na(x)) {
x <- neuprint_search(x, meta = F, field = 'type', fixed=fixed,
conn=conn, dataset=dataset, ...)
}
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20 changes: 19 additions & 1 deletion tests/testthat/test-ids.R
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Original file line number Diff line number Diff line change
Expand Up @@ -33,13 +33,17 @@ test_that("id conversion works", {

toobigid="9223372036854775807"
expect_error(id2bit64(toobigid))
expect_error(id2bit64(-1))
expect_equal(id2bit64(c(1,NA)), bit64::as.integer64(c("1", NA)))
expect_equal(id2bit64(c(1, NA, "")), bit64::as.integer64(c("1", NA, NA)))

expect_equal(id2char(NULL), character(0))
expect_equal(id2char(character(0)), character(0))
expect_equal(id2char(logical(0)), character(0))
expect_equal(id2char(numeric(0)), character(0))
expect_equal(id2char(factor()), character(0))
expect_error(id2char(""))
expect_equal(id2char(""), NA_character_)
expect_equal(id2char(NA), NA_character_)

expect_equal(neuprint_ids(bigid), bigid)
expect_equal(neuprint_ids(1:4), as.character(1:4))
Expand All @@ -48,8 +52,22 @@ test_that("id conversion works", {
expect_error(neuprint_ids(-1))
expect_error(neuprint_ids(numeric()))
expect_equal(neuprint_ids(numeric(), mustWork = FALSE), character())
expect_error(neuprint_ids(NA))
expect_equal(neuprint_ids(NA, mustWork = F), NA_character_)
})

test_that("valid_id works", {
expect_true(valid_id(1))
expect_false(valid_id(NA))
expect_false(valid_id(NULL))
expect_false(valid_id(logical()))
expect_false(valid_id(-1))
toobigid="9223372036854775807"
expect_false(valid_id(toobigid))
})


skip_if_offline()
skip_if(as.logical(Sys.getenv("SKIP_NP_SERVER_TESTS")))

test_that("neuprint_ids works", {
Expand Down