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Catching errors and notes

Marek Gierlinski authored on 14/06/2024 10:33:19
Showing 2 changed files

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@@ -99,16 +99,17 @@ parse_obo_file <- function(obo) {
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 #' @noRd
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 extract_obo_terms <- function(parsed) {
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   # Binding variables from non-standard evaluation locally
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-  key <- term_id <- value <- term_name <- NULL
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+  key <- term_id <- value <- name <- term_name <- namespace <- NULL
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   terms <- parsed |>
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-    dplyr::filter(key == "name") |>
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-    dplyr::select(term_id, term_name = value)
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+    dplyr::filter(key %in% c("name", "namespace")) |>
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+    tidyr::pivot_wider(id_cols = term_id, names_from = key, values_from = value) |>
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+    dplyr::rename(term_name = name)
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   alt_terms <- parsed |>
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     dplyr::filter(key == "alt_id") |>
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     dplyr::left_join(terms, by = "term_id") |>
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-    dplyr::select(term_id = value, term_name)
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+    dplyr::select(term_id = value, term_name, namespace)
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   dplyr::bind_rows(
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     terms,
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@@ -9,16 +9,9 @@ test_that("Incorrect species in fetch_go", {
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   expect_error(fetch_go(species = "not a species"))
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 })
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-
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-test_that("Incorrect mart in fetch_go", {
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-  expect_error(fetch_go(mart = 1))
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-  expect_error(fetch_go(mart = "mart"))
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-})
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-
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-
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 test_that("Incorrect dataset triggers error", {
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   expect_error(fetch_go(dataset = "not a dataset"))
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-  expect_error(fetch_go_from_bm(dataset = "not a dataset"))
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+  expect_error(fetch_go_from_bm(dataset = "not a dataset", use_cache = FALSE, on_error = "stop"))
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 })
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 test_that("Processing OBO file", {