Taxon patch

.zenodo.json

@@ -12,6 +12,11 @@
          "affiliation": "University of Copenhagen",
          "name": "Borregaard, Michael",
          "orcid": "0000-0002-8146-8435"
+      },
+      {
+         "affiliation": "Ghent University",
+         "name": "Stock, Michiel",
+         "orcid": "0000-0003-0903-6061"
       }
    ],
    "access_right": "open",

src/taxon.jl

@@ -80,3 +80,27 @@ function taxon(name::String;
    end
 
 end
+
+"""
+**Get information about a taxon at any level using taxonID**
+
+    taxon(id::Int)
+
+This function will look for a taxon by its taxonID in the GBIF
+reference taxonomy.
+"""
+function taxon(id::Int)
+   args = Dict{String, Any}("id" => id)
+
+   sp_s_url = gbifurl * "species/$id"
+   sp_s_req = HTTP.get(sp_s_url, query=args)
+   if sp_s_req.status == 200
+      body = JSON.parse(String(sp_s_req.body))
+      return GBIFTaxon(body)
+   else
+      throw(ErrorException("Impossible to retrieve information for taxonID $(id) -- HTML error code $(sp_s_req.status)"))
+   end
+
+end
+
+taxon(t::Pair) = taxon(t.second)

src/types/GBIFTaxon.jl

@@ -42,7 +42,7 @@ struct GBIFTaxon
    family::Union{Missing, Pair{String, Int64}}
    genus::Union{Missing, Pair{String, Int64}}
    species::Union{Missing, Pair{String, Int64}}
-   confidence::Int64
+   confidence::Union{Missing, Int64}
    synonym::Bool
 end
 
@@ -59,16 +59,16 @@ function GBIFTaxon(o::Dict{String, Any})
    return GBIFTaxon(
       o["canonicalName"],
       o["scientificName"],
-      Symbol(o["status"]),
-      Symbol(o["matchType"]),
+      Symbol(get(o, "status", "none")),  # returns :none as default
+      Symbol(get(o, "matchType", "none")),
       r["kingdom"],
       r["phylum"],
       r["class"],
       r["order"],
       r["family"],
       r["genus"],
       r["species"],
-      o["confidence"],
+      get(o, "confidence", missing),
       o["synonym"]
    )
 end

test/taxon.jl

@@ -6,6 +6,11 @@ module TestSpecies
   iver = taxon("Iris versicolor", rank=:SPECIES)
   @test iver.species == Pair("Iris versicolor", 5298019)
 
+  iver_id = taxon(5298019)  # test using taxon id
+  @test iver_id.species == iver.species
+
+  @test iver_id == taxon(Pair("Iris versicolor", 5298019))
+
   i_sp = taxon(iver.genus.first; rank=:GENUS, family=iver.family.first, strict=false)
   @test ismissing(i_sp.species)