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Setup

  1. Install Node.js.
  2. Install gnverifier.

Running

When running loir-resources-process, you are sometimes prompted for input. Here are some instructions for this:

Generating Darwin Core failed, retry?

Parsing the text file failed. The reason for this is printed above. The text file can be fixed, after which you can press Enter on the prompt to retry and continue.

Common errors:

  • "levels" should be an array: check the YAML
  • "scope" should be an array: check the YAML
  • Resource contains no taxa: the levels array in the YAML is empty
  • "levels" contains invalid values: check the levels array in the YAML
  • Too much indentation at {line}:0
  • Taxon name ({rank}) should be capitalized: "{taxon}"
  • {rank} should be lowercase: "{taxon}" (can also indicate that the name was parsed wrong)

Source results in short prefix

Sometimes while adding identifiers to the Darwin Core file, two genera with the same name exist and the wrong one is returned. This often results in the two classification paths having a short prefix, for example Animalia for the bird genus Cleptes Gambel, 1847 and the insect genus Cleptes Latreille, 1802.

For Catalogue of Life results this happens a lot, and since the resulting identifiers are not used anyway they are discarded automatically (deleting...). For GBIF results, prompts like are presented:

B123: source 11 results in short prefix "Animalia" (1 taxa)
  taxon: B123:1:1 "Cleptes"
  class: Animalia|Chordata|Aves
  prefx: Animalia|Arthropoda|Insecta|Chrysididae

Here, taxon is the identifier and the name of the taxon currently being resolved; class is the classification of the result of the resolving; and prefx is the classification of the rest of the file.

It then prompts

  Keep or delete (k/d)?

This is because for a key to trees including both pines and oaks already has a short common classification prefix (Plantae|Tracheophyta) in which case the result may be correct even though the prefix is short.

Problems found. Skip or retry?

After this, the remaining results are checked for completeness. If some GBIF taxa are missing they are listed and the following prompt is shown:

B123: problems found in B123:1. Skip or retry (s/r)?

The two options:

  • "Skip" ignores the problem, prompts for the reason (Reason for skipping?) and appends this reason to a global CSV file so that the problem can be ignored automatically in the future.
  • "Retry" reloads the text file and starts parsing and resolving again.