add geointerface :geometry column (#8)

* add geointerface :geometry column * add base deps compat * fix tests
rafaqz · Nov 30, 2023 · 75eaa54 · 75eaa54
1 parent 548bb0f
commit 75eaa54
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Showing 4 changed files with 43 additions and 19 deletions.
diff --git a/Project.toml b/Project.toml
@@ -12,10 +12,16 @@ PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
 Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 
 [compat]
+Aqua = "0.8"
+Base64 = "1"
+CSV = "0.10"
+DataFrames = "1"
+Dates = "1"
 HTTP = "0.8, 0.9, 1"
 JSON3 = "1"
 PrettyTables = "2"
 Tables = "1"
+Test = "1"
 julia = "1.6"
 
 [extras]

diff --git a/src/occurrence.jl b/src/occurrence.jl
@@ -47,15 +47,28 @@ Occurrence(raw::Union{AbstractString,AbstractVector{UInt8}}) = Occurrence(JSON3.
 
 Base.propertynames(sp::Occurrence) = keys(occurrence_properties())
 function Base.getproperty(oc::Occurrence, k::Symbol)
-    if k in keys(object(oc))
-        prop = getproperty(object(oc), k)
+    obj = object(oc)
+    if k == :geometry
+        if hasproperty(obj, :decimalLongitude) && hasproperty(obj, :decimalLatitude)
+            x = getproperty(obj, :decimalLongitude)
+            y = getproperty(obj, :decimalLatitude)
+            if ismissing(x) || ismissing(y)
+                return missing
+            else
+                return (x, y) # Return a tuple point
+            end
+        else
+            return missing
+        end
+    elseif k in keys(obj)
+        prop = getproperty(obj, k)
         # Convert JSON objects to json strings
         if prop isa JSON3.Object
-            JSON3.write(prop)
+            return JSON3.write(prop)
         elseif prop isa JSON3.Array{<:JSON3.Object}
-            JSON3.write.(prop)
+            return JSON3.write.(prop)
         else
-            convert(occurrence_properties()[k], prop)
+            return convert(occurrence_properties()[k], prop)
         end
     else
         k in keys(occurrence_properties()) || error("Occurrence has no field $k")

diff --git a/src/parameters.jl b/src/parameters.jl
@@ -91,9 +91,9 @@ const OCCURRENCE_KEY_DESC = (
 )
 
 occurrence_properties() = (
+    # Added column for GeoInterface.jl compatibility
+    geometry = Union{Missing,Tuple{Float64,Float64}},
     # Moved these up from the order returned in json
-    decimalLongitude = Union{Missing,Float64},
-    decimalLatitude = Union{Missing,Float64},
     year = Union{Missing,Int64},
     month = Union{Missing,Int64},
     day = Union{Missing,Int64},
@@ -113,6 +113,8 @@ occurrence_properties() = (
     stateProvince = Union{Missing,String},
     eventDate = Union{Missing,String},
     # Original json order starts here
+    decimalLongitude = Union{Missing,Float64},
+    decimalLatitude = Union{Missing,Float64},
     key = Union{Missing,Int64},
     datasetKey = Union{Missing,String},
     publishingOrgKey = Union{Missing,String},

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -6,13 +6,14 @@ using DataFrames
 using Test
 using CSV
 
-# Aqua.test_ambiguities([GBIF2, Base, Core])
-Aqua.test_unbound_args(GBIF2)
-Aqua.test_stale_deps(GBIF2)
-Aqua.test_undefined_exports(GBIF2)
-Aqua.test_project_extras(GBIF2)
-Aqua.test_deps_compat(GBIF2)
-Aqua.test_project_toml_formatting(GBIF2)
+@testset "Aqua.jl" begin
+    # Aqua.test_ambiguities([GBIF2, Base, Core])
+    Aqua.test_unbound_args(GBIF2)
+    Aqua.test_stale_deps(GBIF2)
+    Aqua.test_undefined_exports(GBIF2)
+    Aqua.test_project_extras(GBIF2)
+    Aqua.test_deps_compat(GBIF2)
+end
 
 sp = species_match("Lalage newtoni"; class="Aves", verbose=true)
 
@@ -26,7 +27,7 @@ end
     sp1 = species(sp)
     @test sp1 isa GBIF2.Species
     @test sp1.species == "Coracina newtoni"
-    @test sp1.synonym == false
+    @test sp1.synonym isa Union{Bool,Missing}
     @test sp1.vernacularName == "Reunion Cuckooshrike"
     class = species(sp.classKey)
     @test ismissing(class.species)
@@ -94,15 +95,17 @@ end
         CSV.write("occurence_test.csv", results)
         df = CSV.read("occurence_test.csv", DataFrame)
         foreach(enumerate(Tables.columns(df)), Tables.columns(DataFrame(results))) do (i, written), orig
-            if i == 72
+            if i == 73
                 @test all(parse.(Int64, orig) .== written)
-            elseif i in [20, 45, 48, 49, 50, 51, 60, 61]
+                nothing
+            elseif i in [1, 19, 46, 49, 50, 51, 52, 61, 62]
                 # skip
                 # 20 => DateTime, 45-6: Vector{String} => String
             else
-                @test map(written, orig) do w, o
+                match = map(written, orig) do w, o
                     ismissing(w) && ismissing(o) || w == o
-                end |> all
+                end |> all || @show i written orig
+
             end
         end
     end