Version 1.0.8. Improving error handling

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: fenr
 Title: Fast functional enrichment for interactive applications
-Version: 1.1.7
+Version: 1.1.8
 Authors@R: person(
     given = "Marek",
     family = "Gierlinski",

NAMESPACE

@@ -15,6 +15,7 @@ export(functional_enrichment)
 export(get_feature_terms)
 export(get_term_features)
 export(prepare_for_enrichment)
+export(remove_cache)
 importFrom(assertthat,assert_that)
 importFrom(assertthat,is.count)
 importFrom(assertthat,is.string)

NEWS.md

@@ -150,4 +150,9 @@
 ## Version 1.0.7
 
  - Improved error handling with unresponsive servers - timeouts are now handled gracefully
-
+
+## Version 1.0.8
+
+ - Further improving error handling, making sure `assert_url_path()` handles timeouts properly
+ - Introduced on_error = "ignore" for test purposes
+

R/bioplanet.R

@@ -12,15 +12,14 @@ get_bioplanet_pathway_file <- function() {
 #' (NCBI gene ID, gene symbol and pathway ID) from BioPlanet.
 #'
 #' @param use_cache Logical, if TRUE, the remote file will be cached locally.
-#' @param on_error A character vector specifying the error handling method. It
-#'   can take values `"stop"` or `"warn"`. The default is `"stop"`. `"stop"`
-#'   will halt the function execution and throw an error, while `"warn"` will
-#'   issue a warning and return `NULL`.
+#' @param on_error A character string indicating the error handling strategy:
+#'   either "stop" to halt execution, "warn" to issue a warning and return
+#'   `NULL` or "ignore" to return `NULL` without warnings. Defaults to "stop".
 #' @return A list with \code{terms} and \code{mapping} tibbles.
 #' @export
 #' @examples
 #' bioplanet_data <- fetch_bp(on_error = "warn")
-fetch_bp <- function(use_cache = TRUE, on_error = c("stop", "warn")) {
+fetch_bp <- function(use_cache = TRUE, on_error = c("stop", "warn", "ignore")) {
   on_error <- match.arg(on_error)
 
   # Binding variables from non-standard evaluation locally

R/caching.R

@@ -82,11 +82,16 @@ cached_url_path <- function(rname, fpath, use_cache) {
 #' Remove all cache
 #'
 #' This function will remove all cached data used by `fenr`. The user will be
-#' prompted for confirmation. Use with caution!
+#' prompted for confirmation. Use only when you suspect the cache was corrupted.
+#' Use with caution!
 #'
 #' @param ask Logical, whether to ask user for confirmation.
 #' @return TRUE if successfully removed.
-#' @noRd
+#' @export
+#' @examples
+#' \dontrun{
+#' remove_cache()
+#' }
 remove_cache <- function(ask = TRUE) {
   cache <- cache_location()
   bfc <- BiocFileCache::BiocFileCache(cache, ask = FALSE)

R/go.R

@@ -112,14 +112,13 @@ extract_obo_terms <- function(parsed) {
 #' Download GO term descriptions
 #'
 #' @param use_cache Logical, if TRUE, the remote file will be cached locally.
-#' @param on_error A character vector specifying the error handling method. It
-#'   can take values `"stop"` or `"warn"`. The default is `"stop"`. `"stop"`
-#'   will halt the function execution and throw an error, while `"warn"` will
-#'   issue a warning and return `FALSE`.
+#' @param on_error A character string indicating the error handling strategy:
+#'   either "stop" to halt execution, "warn" to issue a warning and return
+#'   `NULL` or "ignore" to return `NULL` without warnings. Defaults to "stop".
 #'
 #' @return A tibble with term_id and term_name.
 #' @noRd
-fetch_go_terms <- function(use_cache, on_error = "stop") {
+fetch_go_terms <- function(use_cache, on_error) {
   obo_file <- get_go_obo_file()
   if(!assert_url_path(obo_file, on_error))
     return(NULL)
@@ -142,16 +141,15 @@ fetch_go_terms <- function(use_cache, on_error = "stop") {
 #' without extension (e.g. for a file \file{goa_chicken.gaf} the designation is
 #' \file{goa_chicken}).
 #'
-#' @param on_error A character vector specifying the error handling method. It
-#'   can take values `"stop"` or `"warn"`. The default is `"stop"`. `"stop"`
-#'   will halt the function execution and throw an error, while `"warn"` will
-#'   issue a warning and return `NULL`.
+#' @param on_error A character string indicating the error handling strategy:
+#'   either "stop" to halt execution, "warn" to issue a warning and return
+#'   `NULL` or "ignore" to return `NULL` without warnings. Defaults to "stop".
 #'
 #' @return A tibble with columns \code{species} and \code{designation}.
 #' @export
 #' @examples
 #' go_species <- fetch_go_species(on_error = "warn")
-fetch_go_species <- function(on_error = c("stop", "warn")) {
+fetch_go_species <- function(on_error = c("stop", "warn", "ignore")) {
   on_error <- match.arg(on_error)
   # Binding variables from non-standard evaluation locally
   species <- designation <- `Species/Database` <- File <- NULL
@@ -184,14 +182,13 @@ fetch_go_species <- function(on_error = c("stop", "warn")) {
 #'   \url{http://current.geneontology.org/annotations}. Examples are
 #'   \file{goa_human} for human, \file{mgi} for mouse or \file{sgd} for yeast.
 #' @param use_cache Logical, if TRUE, the remote file will be cached locally.
-#' @param on_error A character vector specifying the error handling method. It
-#'   can take values `"stop"` or `"warn"`. The default is `"stop"`. `"stop"`
-#'   will halt the function execution and throw an error, while `"warn"` will
-#'   issue a warning and return `NULL`.
+#' @param on_error A character string indicating the error handling strategy:
+#'   either "stop" to halt execution, "warn" to issue a warning and return
+#'   `NULL` or "ignore" to return `NULL` without warnings. Defaults to "stop".
 #'
 #' @return A tibble with columns \code{gene_symbol}, \code{uniprot_id} and \code{term_id}.
 #' @noRd
-fetch_go_genes_go <- function(species, use_cache, on_error = "stop") {
+fetch_go_genes_go <- function(species, use_cache, on_error) {
   # Binding variables from non-standard evaluation locally
   gene_id <- db_object_synonym <- symbol <- NULL
   db_id <- go_term <- NULL
@@ -228,23 +225,24 @@ fetch_go_genes_go <- function(species, use_cache, on_error = "stop") {
 #'   species can be obtained using \code{fetch_go_species} - column
 #'   \code{designation}.
 #' @param use_cache Logical, if TRUE, the remote file will be cached locally.
-#' @param on_error A character vector specifying the error handling method. It
-#'   can take values `"stop"` or `"warn"`. The default is `"stop"`. `"stop"`
-#'   will halt the function execution and throw an error, while `"warn"` will
-#'   issue a warning and return `NULL`.
+#' @param on_error A character string indicating the error handling strategy:
+#'   either "stop" to halt execution, "warn" to issue a warning and return
+#'   `NULL` or "ignore" to return `NULL` without warnings. Defaults to "stop".
 #'
 #' @return A list with \code{terms} and \code{mapping} tibbles.
 #' @importFrom assertthat assert_that
 #' @noRd
-fetch_go_from_go <- function(species, use_cache, on_error = "stop") {
+fetch_go_from_go <- function(species, use_cache, on_error) {
   assert_that(!missing(species), msg = "Argument 'species' is missing.")
   assert_species(species, "fetch_go_species", on_error)
 
   mapping <- fetch_go_genes_go(species = species, use_cache = use_cache, on_error = on_error)
   if(is.null(mapping))
     return(NULL)
 
-  terms <- fetch_go_terms(use_cache = use_cache)
+  terms <- fetch_go_terms(use_cache = use_cache, on_error = on_error)
+  if(is.null(terms))
+    return(NULL)
 
   list(
     terms = terms,
@@ -261,15 +259,14 @@ fetch_go_from_go <- function(species, use_cache, on_error = "stop") {
 #'   biomaRt::useEnsembl(biomart = "ensembl"), followed by
 #'   biomaRt::listDatasets(mart).
 #' @param use_cache Logical, if TRUE, the remote data will be cached locally.
-#' @param on_error A character vector specifying the error handling method. It
-#'   can take values `"stop"` or `"warn"`. The default is `"stop"`. `"stop"`
-#'   will halt the function execution and throw an error, while `"warn"` will
-#'   issue a warning and return `NULL`.
+#' @param on_error A character string indicating the error handling strategy:
+#'   either "stop" to halt execution, "warn" to issue a warning and return
+#'   `NULL` or "ignore" to return `NULL` without warnings. Defaults to "stop".
 #'
 #' @return A tibble with columns \code{gene_id}, \code{gene_symbol} and
 #'   \code{term_id}.
 #' @noRd
-fetch_go_genes_bm <- function(dataset, use_cache = TRUE, on_error = c("stop", "warn")) {
+fetch_go_genes_bm <- function(dataset, use_cache, on_error) {
   xml <- get_biomart_xml(dataset) |>
     stringr::str_replace_all("\\s", "%20")
   req <- paste0(get_biomart_url(), "/biomart/martservice?query=", xml)
@@ -298,15 +295,14 @@ fetch_go_genes_bm <- function(dataset, use_cache = TRUE, on_error = c("stop", "w
 #'   biomaRt::useEnsembl(biomart = "ensembl"), followed by
 #'   biomaRt::listDatasets(mart).
 #' @param use_cache Logical, if TRUE, the remote file will be cached locally.
-#' @param on_error A character vector specifying the error handling method. It
-#'   can take values `"stop"` or `"warn"`. The default is `"stop"`. `"stop"`
-#'   will halt the function execution and throw an error, while `"warn"` will
-#'   issue a warning and return `NULL`.
+#' @param on_error A character string indicating the error handling strategy:
+#'   either "stop" to halt execution, "warn" to issue a warning and return
+#'   `NULL` or "ignore" to return `NULL` without warnings. Defaults to "stop".
 #'
 #' @importFrom assertthat assert_that is.string
 #' @return A list with \code{terms} and \code{mapping} tibbles.
 #' @noRd
-fetch_go_from_bm <- function(dataset, use_cache = TRUE, on_error = c("stop", "warn")) {
+fetch_go_from_bm <- function(dataset, use_cache, on_error) {
   assert_that(!missing(dataset), msg = "Argument 'dataset' is missing.")
   assert_that(is.string(dataset))
 
@@ -353,10 +349,9 @@ fetch_go_from_bm <- function(dataset, use_cache = TRUE, on_error = c("stop", "wa
 #'   biomaRt::useEnsembl(biomart = "ensembl"), followed by
 #'   biomaRt::listDatasets(mart).
 #' @param use_cache Logical, if TRUE, the remote data will be cached locally.
-#' @param on_error A character vector specifying the error handling method. It
-#'   can take values `"stop"` or `"warn"`. The default is `"stop"`. `"stop"`
-#'   will halt the function execution and throw an error, while `"warn"` will
-#'   issue a warning and return `NULL`.
+#' @param on_error A character string indicating the error handling strategy:
+#'   either "stop" to halt execution, "warn" to issue a warning and return
+#'   `NULL` or "ignore" to return `NULL` without warnings. Defaults to "stop".
 #'
 #' @return A list with \code{terms} and \code{mapping} tibbles.
 #' @export
@@ -366,7 +361,8 @@ fetch_go_from_bm <- function(dataset, use_cache = TRUE, on_error = c("stop", "wa
 #' go_data_ensembl <- fetch_go(dataset = "scerevisiae_gene_ensembl", on_error = "warn")
 #' # Fetch GO data from Gene Ontology
 #' go_data_go <- fetch_go(species = "sgd", on_error = "warn")
-fetch_go <- function(species = NULL, dataset = NULL, use_cache = TRUE, on_error = c("stop", "warn")) {
+fetch_go <- function(species = NULL, dataset = NULL, use_cache = TRUE,
+                     on_error = c("stop", "warn", "ignore")) {
   on_error <- match.arg(on_error)
 
   assert_that(!(is.null(species) & is.null(dataset)),

R/interactive_example.R

@@ -6,8 +6,10 @@
 #' @return A list of objects containing functional terms for GO and Reactome.
 #' @export
 #' @examples
+#' \dontrun{
 #' data(yeast_de)
 #' term_data <- fetch_terms_for_example(yeast_de)
+#' }
 fetch_terms_for_example <- function(de) {
   # All gene background
   all_genes <- de$gene_id
@@ -19,7 +21,7 @@ fetch_terms_for_example <- function(de) {
 
   # load Reactome pathways
   message("Fetching Reactome data\n")
-  re <- fetch_reactome("Saccharomyces cerevisiae", on_error = "warn")
+  re <- fetch_reactome("Saccharomyces cerevisiae")
   re_data <- prepare_for_enrichment(re$terms, re$mapping, all_genes, feature_name = "gene_id")
 
   # Put all functional term data in one structure; Shiny app will access
@@ -173,9 +175,9 @@ main_plot <- function(de, input) {
 #' @importFrom assertthat assert_that
 #' @export
 #' @examples
+#' \dontrun{
 #' data(yeast_de)
 #' term_data <- fetch_terms_for_example(yeast_de)
-#' if(interactive()) {
 #'   enrichment_interactive(yeast_de, term_data)
 #' }
 enrichment_interactive <- function(de, term_data) {

R/kegg.R

@@ -9,17 +9,16 @@ get_kegg_url <- function() {
 
 #' Find all species available from KEGG
 #'
-#' @param on_error A character vector specifying the error handling method. It
-#'   can take values `"stop"` or `"warn"`. The default is `"stop"`. `"stop"`
-#'   will halt the function execution and throw an error, while `"warn"` will
-#'   issue a warning and return `NULL`.
+#' @param on_error A character string indicating the error handling strategy:
+#'   either "stop" to halt execution, "warn" to issue a warning and return
+#'   `NULL` or "ignore" to return `NULL` without warnings. Defaults to "stop".
 #'
 #' @return A tibble, in which column \code{designation} contains species
 #'   designations used in function \code{fetch_kegg}.
 #' @export
 #' @examples
 #' spe <- fetch_kegg_species(on_error = "warn")
-fetch_kegg_species <- function(on_error = c("stop", "warn")) {
+fetch_kegg_species <- function(on_error = c("stop", "warn", "ignore")) {
   on_error <- match.arg(on_error)
 
   resp <- http_request(get_kegg_url(), "list/organism")
@@ -34,10 +33,9 @@ fetch_kegg_species <- function(on_error = c("stop", "warn")) {
 #' Download pathway data from KEGG
 #'
 #' @param species A valid species designation used by KEGG.
-#' @param on_error A character vector specifying the error handling method. It
-#'   can take values `"stop"` or `"warn"`. The default is `"stop"`. `"stop"`
-#'   will halt the function execution and throw an error, while `"warn"` will
-#'   issue a warning and return `NULL`.
+#' @param on_error A character string indicating the error handling strategy:
+#'   either "stop" to halt execution, "warn" to issue a warning and return
+#'   `NULL` or "ignore" to return `NULL` without warnings. Defaults to "stop".
 #'
 #' @return A tibble with columns \code{gene_id} and \code{term_id}.
 #' @noRd
@@ -118,14 +116,13 @@ parse_kegg_genes <- function(s) {
 #' @param pathways A character vector with KEGG pathways
 #' @param batch_size Number of pathways sent to KEGG database in one query. The
 #'   maximum allowed is 10.
-#' @param on_error A character vector specifying the error handling method. It
-#'   can take values `"stop"` or `"warn"`. The default is `"stop"`. `"stop"`
-#'   will halt the function execution and throw an error, while `"warn"` will
-#'   issue a warning and return `NULL`.
+#' @param on_error A character string indicating the error handling strategy:
+#'   either "stop" to halt execution, "warn" to issue a warning and return
+#'   `NULL` or "ignore" to return `NULL` without warnings. Defaults to "stop".
 #' @importFrom assertthat assert_that
 #' @return A tibble with columns \code{gene_id} and \code{term_id}
 #' @noRd
-fetch_kegg_mapping <- function(pathways, batch_size, on_error = "stop") {
+fetch_kegg_mapping <- function(pathways, batch_size, on_error) {
   assert_that(is.character(pathways))
   batches <- split(pathways, ceiling(seq_along(pathways) / batch_size))
 
@@ -167,17 +164,16 @@ fetch_kegg_mapping <- function(pathways, batch_size, on_error = "stop") {
 #'   full list of available KEGG species can be found by using \code{fetch_kegg_species}.
 #' @param batch_size Number of pathways sent to KEGG database in one query. The
 #'   maximum allowed is 10.
-#' @param on_error A character vector specifying the error handling method. It
-#'   can take values `"stop"` or `"warn"`. The default is `"stop"`. `"stop"`
-#'   will halt the function execution and throw an error, while `"warn"` will
-#'   issue a warning and return `NULL`.
+#' @param on_error A character string indicating the error handling strategy:
+#'   either "stop" to halt execution, "warn" to issue a warning and return
+#'   `NULL` or "ignore" to return `NULL` without warnings. Defaults to "stop".
 #'
 #' @return A list with \code{terms} and \code{mapping} tibbles.
 #' @importFrom assertthat assert_that is.count
 #' @export
 #' @examples
 #' kegg_data <- fetch_kegg("mge", on_error = "warn")
-fetch_kegg <- function(species, batch_size = 10, on_error = c("stop", "warn")) {
+fetch_kegg <- function(species, batch_size = 10, on_error = c("stop", "warn", "ignore")) {
   on_error <- match.arg(on_error)
 
   assert_that(!missing(species), msg = "Argument 'species' is missing.")