Skip to content

fix: handle comments properly instead of hard-coding skips #67

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
mtran-code merged 3 commits into from
Oct 21, 2025
Merged

fix: handle comments properly instead of hard-coding skips #67

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
e1daecd
fix: properly skip tsv comments instead of hardcoding skips
mtran-code Oct 21, 2025
10fe414
refactor: streamline cellosaurus column ordering
mtran-code Oct 21, 2025
6b1e9af
chore: restore cellosaurus column ordering
mtran-code Oct 21, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 6 additions & 1 deletion R/utils-httr2.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -61,5 +61,10 @@
#' @noRd
#' @keywords internal
.parse_resp_tsv <- function(resp, show_col_types = FALSE, skip = 0) {
readr::read_tsv(resp$body, skip = skip, show_col_types = show_col_types)
readr::read_tsv(
resp$body,
skip = skip,
show_col_types = show_col_types,
comment = "#"
)
}
8 changes: 4 additions & 4 deletions tests/testthat/test_cellosaurus_helpers.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -39,9 +39,9 @@ test_that(".build_cellosaurus_request is acting as expected", {
expect_equal(request$url, expected)

response <- AnnotationGx:::.perform_request(request) |>
AnnotationGx:::.parse_resp_tsv(show_col_types = FALSE, skip = 14)
AnnotationGx:::.parse_resp_tsv(show_col_types = FALSE)
expect_class(response, "spec_tbl_df")
expect_gte(nrow(response), 1)
expect_equal(nrow(response), 1)

request2 <- AnnotationGx:::.build_cellosaurus_request(
query = "id:HeLa",
Expand Down Expand Up @@ -74,8 +74,8 @@ test_that(".build_cellosaurus_request is acting as expected", {
"https://api.cellosaurus.org/search/cell-line?q=id%3AHeLa&sort=ac%20asc&fields=id%2Cac%2Csy%2Cacas%2Csx%2Cag%2Cdi%2Cdio%2Cdin%2Cdr%2Ccell-type%2Cderived-from-site%2Cmisspelling%2Cdt%2Cdtc%2Cdtu%2Cdtv%2Cgenome-ancestry&format=tsv&rows=2"
)
response <- AnnotationGx:::.perform_request(request2) |>
AnnotationGx:::.parse_resp_tsv(show_col_types = FALSE, skip = 14)
expect_gte(nrow(response), 1)
AnnotationGx:::.parse_resp_tsv(show_col_types = FALSE)
expect_equal(nrow(response), 2)
})

test_that(".build_cellosaurus_request accepts documented sort fields", {
Expand Down
Loading