Fix #183

Author: damianooldoni

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: trias
 Title: Process Data for the Project Tracking Invasive Alien Species
     (TrIAS)
-Version: 3.2.2
+Version: 3.2.3
 Authors@R: c(
     person("Damiano", "Oldoni", , "damiano.oldoni@inbo.be", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-3445-7562")),

NEWS.md

@@ -1,6 +1,10 @@
+# trias 3.2.3
+
+- Fix a bug in `update_download_list()`. The fix ensures that the function can handle cases where there are no existing downloads without throwing an error (#183). 
+
 # trias 3.2.2
 
-- Fix y-axis ticks values in `visualize_pathways_level1()` and `visualize_pathways_level2()` plots.
+- Fix y-axis ticks values in `visualize_pathways_level1()` and `visualize_pathways_level2()` plots (#181).
 
 # trias 3.2.1
 

R/update_download_list.R

@@ -31,6 +31,21 @@
 #' @export
 update_download_list <- function(file, download_to_add, input_checklist,
                                  url_doi_base = "https://doi.org/") {
+  # `file` must have the right columns
+  expected_columns <- c(
+    "gbif_download_key",
+    "input_checklist",
+    "gbif_download_created",
+    "gbif_download_status",
+    "gbif_download_doi"
+  )
+  assertthat::assert_that(
+    all(expected_columns %in% colnames(readr::read_tsv(file, n_max = 0))),
+    msg = paste(
+      "The file should contain the following columns:",
+      paste(expected_columns, collapse = ", ")
+    )
+  )
   downloads <- readr::read_tsv(file,
     trim_ws = TRUE,
     na = "",
@@ -66,7 +81,6 @@ update_download_list <- function(file, download_to_add, input_checklist,
   } else {
     print(paste("gbif_download_Key", download_to_add, "already present in", file))
   }
-  # check all downloads with status "PREPARING" or "RUNNING".
   changes <- FALSE
   for (i in 1:nrow(downloads)) {
     if (downloads$gbif_download_status[i] %in% c("RUNNING", "PREPARING")) {

tests/testthat/data_test_upload_list/gbif_downloads_wrong_cols.tsv

@@ -0,0 +1 @@
+gbif_download_key input_checklist gbif_download_created	gbif_download_status	gbif_download_doi

tests/testthat/test-update_download_list.R

@@ -1,11 +1,26 @@
+testthat::test_that("Error returned if file does not contain the right columns", {
+  directory_data <- "./data_test_upload_list/"
+  gbif_downloads_filename <- "gbif_downloads_wrong_cols.tsv"
+  gbif_downloads_file <- paste0(directory_data, gbif_downloads_filename)
+  gbif_download_key_to_add <- "0003300-181003121212138"
+  checklist <- "https://raw.githubusercontent.com/trias-project/pipeline/9f20d33a14696bc42d059a2e0f50fb11c4f97d35/data/input/occ_indicator_emerging_species.tsv"
+  testthat::expect_error(
+    update_download_list(
+      file = gbif_downloads_file,
+      download_to_add = gbif_download_key_to_add,
+      input_checklist = checklist
+    ),
+    regexp = "The file should contain the following columns: gbif_download_key, input_checklist, gbif_download_created, gbif_download_status, gbif_download_doi"
+  )
+})
+
 testthat::test_that("gbif download added correctly to list GBIF downloads and other status updated", {
-  skip_on_os(os = "windows")
-  #' define file containing gbif downloads
+  # Define file containing gbif downloads
   directory_data <- "./data_test_upload_list/"
   gbif_downloads_filename <- "gbif_downloads.tsv"
   gbif_downloads_file <- paste0(directory_data, gbif_downloads_filename)
 
-  #' make a coy of it to replace original file at the end of the test
+  # Make a coy of it to replace original file at the end of the test
   gbif_downloads_filename_copy <- "gbif_downloads_copy.tsv"
   copy_file <- paste0(directory_data, gbif_downloads_filename_copy)
   file.copy(
@@ -18,12 +33,12 @@ testthat::test_that("gbif download added correctly to list GBIF downloads and ot
                               na = "",
                               lazy = FALSE)
 
-  #' define arguments related to new GBIF download
+  # Define arguments related to new GBIF download
   gbif_download_key_to_add <- "0003300-181003121212138"
   checklist <- "https://raw.githubusercontent.com/trias-project/pipeline/9f20d33a14696bc42d059a2e0f50fb11c4f97d35/data/input/occ_indicator_emerging_species.tsv"
 
 
-  #' apply update_download_list
+  # Apply update_download_list
   update_download_list(
     file = gbif_downloads_file,
     download_to_add = gbif_download_key_to_add,