Write gbif_download() function

[peterdesmet]

Usage:

gbif_download(
    taxa="https://raw.githubusercontent.com/trias-project/alien-plants-belgium/afbd2805de77afd79fb74669c403d40f1416661b/data/processed/taxon.csv",
    country="BE", # default
    output="../data/output/gbif_downloads.csv" # default
)

The script would:

1. Verify and report errors the parameter checklist:
   • Can it be found
   • Is it a csv file
   • Is it a GitHub commit URL
   • Has the file a column gbif_nubKey
   • Does gbif_nubKey contain numbers only
2. Verify and report errors for the option country:
   • Is it a valid ISO 3166-1 alpha-2
3. Verify and report errors for the option output:
   • Does the file exist
4. Use rgbif to trigger a download
5. Write information to data/output/gbif_downloads.csv:
   • gbif_download_key: GBIF download UUID
   • input_checklist: checklist (parameter)
   • input_country: country (parameter)

[peterdesmet]

Note: function should be part of TrIAS R package, not this repository.

[damianooldoni]

point 1,2,3 not present anymore in the pipeline. But I the checks have been written and I think they are still very useful while merging checklists.

[peterdesmet]

Rather than a function, we opted to use basic R and rgbif functionality: https://github.com/trias-project/pipeline/blob/master/src/occurrences.Rmd. Closing issue.