update_download_list: Update the list with all downloads

In trias-project/trias: Process Data for the Project Tracking Invasive Alien Species (TrIAS)

Update the list with all downloads

Description

This function opens a (tab-separated) text file containing all occurrence downloads from GBIF and updates the status of all downloads with status RUNNING or PREPARING. If the specified download is not present it will be add.

Usage

update_download_list(
  file,
  download_to_add,
  input_checklist,
  url_doi_base = "https://doi.org/"
)

Arguments

file	text file (tab separated) containing all occurrence downloads from GBIF. File should contain the following columns: gbif_download_key: GBIF download keys, e.g. 0012078-181003121212138 input_checklist: filename or link to readable text file containing the list of queried taxa gbif_download_created: datetime of the GBIF download creation as returned by rgbif function occ_download_meta gbif_download_status: status of the GBIF download as returned by as returned by rgbif function occ_download_meta, e.g. RUNNING, PREPARING, SUCCEDEED gbif_download_doi: DOI link as returned by as returned by rgbif function occ_download_meta (e.g. 10.15468/dl.kg0uxf) + url_doi_base value (see below)
download_to_add	character. A GBIF download key to be added to file.
input_checklist	text file with taxon keys whose occurrences you want to download
url_doi_base	character. doi base URL; url_doi_base + doi form a link to a page with download information. Default: "https://doi.org/".

Details

If a download key is passed which is not present in the file it will be added as a new line.

Value

message with the performed updates

trias-project/trias documentation built on Sept. 18, 2024, 11:50 a.m.