eppo_tabletools_distri subscript out of bounds error

Hello,

Thanks for the cool package :)

I've installed the most recent version (0.8.2) and am encountering an error when trying to retrieve pest distributions. I was able to retrieve other metadata (e.g. taxonomy, hosts etc) without problems, but when I try to get distributions, the following error arises:

> pests <- c("Anastrepha ludens", "Drosophila suzukii")
> pests_names_tables <- eppo_names_tables(pests, eppo_SQLite)
> pest_distri <- eppo_tabletools_distri(pests_names_tables, eppo_token)
New names:                                                                                                                 
• `` -> `...6`
• `` -> `...7`
• `` -> `...8`
• `` -> `...9`
• `` -> `...10`
• `` -> `...11`
• `` -> `...12`
• `` -> `...13`
• `` -> `...14`
• `` -> `...15`
• `` -> `...16`
• `` -> `...17`
• `` -> `...18`
• `` -> `...19`
• `` -> `...20`
• `` -> `...21`
• `` -> `...22`
• `` -> `...23`
• `` -> `...24`
• `` -> `...25`
New names:                                                                                                                 
• `` -> `...6`
• `` -> `...7`
• `` -> `...8`
• `` -> `...9`
• `` -> `...10`
• `` -> `...11`
• `` -> `...12`
• `` -> `...13`
• `` -> `...14`
• `` -> `...15`
• `` -> `...16`
• `` -> `...17`
• `` -> `...18`
• `` -> `...19`
• `` -> `...20`
• `` -> `...21`
• `` -> `...22`
• `` -> `...23`
• `` -> `...24`
• `` -> `...25`
The distribution file for EPPO code ANSTLU was not found.
The distribution file for EPPO code DROSSU was not found.
Error in distri_lists[[i]] : subscript out of bounds

It appears that the eppocodes and URLs are being generated as expected:

Browse[1]> eppocodes
[1] "ANSTLU" "DROSSU"
Browse[1]> distri_urls
[1] "https://gd.eppo.int/taxon/ANSTLU/download/distribution_csv" "https://gd.eppo.int/taxon/DROSSU/download/distribution_csv"
Browse[1]> names_tables$exist_in_DB
  codeid           fullname
1   4669  Anastrepha ludens
2   9518 Drosophila suzukii

When I do a manual search on the EPPO website, the data is there. When I paste the above URLs into a browser window, the files download and contain data. However, the column format of the EPPO file appears different to the expected by pestr - in addition to the columns "continent", "country", "state","country code", "state code", "Status", there are now also several other unnamed columns.

I think this is causing eppo_csv_download to throw an error at this point:

if (!all(names(distri_lists[[i]]) %in%
             c("continent", "country", "state",
               "country code", "state code", "Status"))) {
      message(msg_helper("no_distri", i))
      distri_lists[[i]] <- NULL

When I run the preceding code in debug mode it seems to work ok:

Browse[1]> for (i in 1:length(distri_lists)) {
+     distri_lists[[i]] <- eppo_try_urls(distri_urls[i]) %>%
+         httr::content(type = "text/csv",
+                       encoding = "UTF-8",
+                       col_types = readr::cols()) %>%
+         as.data.frame()
+ }
New names:                                                                                                                 
• `` -> `...6`
• `` -> `...7`
• `` -> `...8`
• `` -> `...9`
• `` -> `...10`
• `` -> `...11`
• `` -> `...12`
• `` -> `...13`
• `` -> `...14`
• `` -> `...15`
• `` -> `...16`
• `` -> `...17`
• `` -> `...18`
• `` -> `...19`
• `` -> `...20`
• `` -> `...21`
• `` -> `...22`
• `` -> `...23`
• `` -> `...24`
• `` -> `...25`
New names:                                                                                                                 
• `` -> `...6`
• `` -> `...7`
• `` -> `...8`
• `` -> `...9`
• `` -> `...10`
• `` -> `...11`
• `` -> `...12`
• `` -> `...13`
• `` -> `...14`
• `` -> `...15`
• `` -> `...16`
• `` -> `...17`
• `` -> `...18`
• `` -> `...19`
• `` -> `...20`
• `` -> `...21`
• `` -> `...22`
• `` -> `...23`
• `` -> `...24`
• `` -> `...25`
Browse[1]> distri_lists[["DROSSU"]][1,]
  country   state country code state code Status                             ...6 ...7 ...8 ...9 ...10 ...11 ...12 ...13
1  Africa Algeria         <NA>         DZ   <NA> Present, restricted distribution   NA   NA   NA    NA    NA    NA    NA
  ...14 ...15 ...16 ...17 ...18 ...19 ...20 ...21 ...22 ...23 ...24 ...25 continent
1    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA        NA

Lastly, I noticed that EPPO seems to have scrambled the column order - 'continent' is the last column name, but the continent data is in the first column.

Thanks!

mczyzj / pestr

eppo_tabletools_distri subscript out of bounds error #26