Code tidy-up

bartongroup · Dec 14, 2023 · e59c3e4 · e59c3e4
1 parent 9669064
commit e59c3e4
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Showing 6 changed files with 3 additions and 24 deletions.
diff --git a/R/go.R b/R/go.R
@@ -96,9 +96,6 @@ extract_obo_terms <- function(parsed) {
 #' @return A tibble with term_id and term_name.
 #' @noRd
 fetch_go_terms <- function(use_cache, on_error = "stop") {
-  # Temporary patch to circumvent vroom 1.6.4 bug
-  # readr::local_edition(1)
-
   obo_file <- get_go_obo_file()
   if(!assert_url_path(obo_file, on_error))
     return(NULL)
@@ -175,15 +172,12 @@ fetch_go_genes_go <- function(species, use_cache, on_error = "stop") {
   gene_synonym <- db_object_synonym <- symbol <- NULL
   db_id <- go_term <- NULL
 
-  # Temporary patch to circumvent vroom 1.6.4 bug
-  # readr::local_edition(1)
-
   url <- get_go_annotation_url()
   gaf_file <- stringr::str_glue("{url}/{species}.gaf.gz")
   if(!assert_url_path(gaf_file, on_error))
     return(NULL)
 
-  lpath <- cached_url_path(stringr::str_glue("gaf_{species}"), gaf_file, use_cache)
+  lpath <- cached_url_path(stringr::str_glue("go_gaf_{species}"), gaf_file, use_cache)
   readr::read_tsv(lpath, comment = "!", quote = "", col_names = GAF_COLUMNS,
                   col_types = GAF_TYPES) |>
     dplyr::mutate(gene_synonym = stringr::str_remove(db_object_synonym, "\\|.*$")) |>

diff --git a/R/kegg.R b/R/kegg.R
@@ -20,10 +20,6 @@ get_kegg_url <- function() {
 #' @examples
 #' spe <- fetch_kegg_species()
 fetch_kegg_species <- function(on_error = c("stop", "warn")) {
-
-  # Temporary patch to circumvent vroom 1.6.4 bug
-  # readr::local_edition(1)
-
   qry <- api_query(get_kegg_url(), "list/organism")
   if(qry$is_error)
     return(catch_error("KEGG", qry$response, on_error))
@@ -47,9 +43,6 @@ fetch_kegg_pathways <- function(species, on_error) {
   # Binding variables from non-standard evaluation locally
   term_id <- NULL
 
-  # Temporary patch to circumvent vroom 1.6.4 bug
-  # readr::local_edition(1)
-
   qry <- api_query(get_kegg_url(), stringr::str_glue("list/pathway/{species}"))
   if(qry$is_error)
     return(catch_error("KEGG", qry$response, on_error))

diff --git a/R/reactome.R b/R/reactome.R
@@ -100,9 +100,6 @@ fetch_reactome_ensembl_genes <- function(spec, use_cache = TRUE, on_error = "sto
   # Binding variables from non-standard evaluation locally
   species <- gene_id <- term_id <- NULL
 
-  # Temporary patch to circumvent vroom 1.6.4 bug
-  # readr::local_edition(1)
-
   ensembl_file <- get_reactome_ensembl_file()
   if(!assert_url_path(ensembl_file, on_error))
     return(NULL)
@@ -130,9 +127,6 @@ fetch_reactome_gene_association <- function(tax_id, use_cache = TRUE, on_error =
   # Binding variables from non-standard evaluation locally
   symbol <- taxon <- db_ref <- db_id <- NULL
 
-  # Temporary patch to circumvent vroom 1.6.4 bug
-  # readr::local_edition(1)
-
   gaf_file <- get_reactome_gaf_file()
   if(!assert_url_path(gaf_file, on_error))
     return(NULL)

diff --git a/R/util.R b/R/util.R
@@ -1,3 +1,4 @@
+# Gene Annotation File column names. GAF is used by GO and Reactome.
 GAF_COLUMNS <- c(
   "db",
   "db_id",

diff --git a/tests/test_data/kegg_parseing_result.rds → tests/test_data/kegg_parsing_result.rds b/tests/test_data/kegg_parseing_result.rds → tests/test_data/kegg_parsing_result.rds
diff --git a/tests/testthat/test_kegg.R b/tests/testthat/test_kegg.R
@@ -13,11 +13,8 @@ test_that("Incorrect batch size in fetch_kegg", {
 
 
 test_that("Parsing KEGG flat file", {
-  # Temporary patch to circumvent vroom 1.6.4 bug
-  # readr::local_edition(1)
-
   flat <- readr::read_file("../test_data/kegg_test.txt")
-  expected <- readr::read_rds("../test_data/kegg_parseing_result.rds")
+  expected <- readr::read_rds("../test_data/kegg_parsing_result.rds")
   parsed <- parse_kegg_genes(flat)
   expect_equal(parsed, expected)
 })