Fix the GBIF issue for single argument queries (#166)

* 🐛add tests to capture #165

* update README

* ✅ fix a bug due to GBIF re-adding a formerly missing occurrence

* ⚠️  add error when the value is not part of the enum key

* 🐛 update the imported modules for edgecase test

* ℹ️ add a temporary log to see the query string

* ✅ the tests are passing

Closes #165

GBIF/Project.toml

@@ -1,7 +1,7 @@
 name = "GBIF"
 uuid = "ee291a33-5a6c-5552-a3c8-0f29a1181037"
 authors = ["Timothée Poisot <timothee.poisot@umontreal.ca>"]
-version = "0.4.1"
+version = "0.4.2"
 
 [deps]
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"

GBIF/README.md

@@ -1,8 +1,9 @@
 # GBIF wrapper for Julia
 
-This is project offers an interface to the [GBIF] search API from
+This is project offers an interface to the GBIF search API from
 Julia. Current efforts focus on querying and exporting occurrences through the
 `occurrence/search` endpoint. There is partial support for the taxonomic API.
 
 The recommended way to use this package is through the
-`SpeciesDistributionToolkit` package.
+`SpeciesDistributionToolkit` package, which will transparently export all of the
+`GBIF` types and methods.

GBIF/src/occurrence.jl

@@ -1,3 +1,4 @@
+format_querypair_stem(stem::Bool) = replace(string(stem), " " => "%20")
 format_querypair_stem(stem::Any) = replace(string(stem), " " => "%20")
 
 function format_querypair_stem(stem::Tuple{T, T}) where {T <: Number}
@@ -44,7 +45,9 @@ function occurrence(key::String)::GBIFRecord
         return GBIFRecord(result)
     catch err
         if err isa HTTP.Exceptions.StatusError
-            throw("Occurrence $(key) (at $(occ_url)) cannot be accessed - error code: $(err.status)")
+            throw(
+                "Occurrence $(key) (at $(occ_url)) cannot be accessed - error code: $(err.status)",
+            )
         else
             throw("Occurrence $(key) cannot be accessed")
         end

GBIF/src/query.jl

@@ -85,6 +85,8 @@ function validate_occurrence_query(query::Pair)
 
     # ENUMs
     if query.first ∈ keys(gbifenums)
-        @assert query.second ∈ gbifenums[query.first]
+        if !(query.second ∈ gbifenums[query.first])
+            @error "The value $(query.second) is not a valid value for $(query.first)"
+        end
     end
 end

GBIF/test/edgecases.jl

@@ -0,0 +1,13 @@
+module GBIFEdgeCasesTest
+using Test
+using GBIF
+
+# When there is a single argument used for a query, sometimes the second position gets
+# converted to not text
+queryset = ["hasCoordinate" => true]
+@test length(occurrences(queryset...)) > 0
+
+queryset = ["hasCoordinate" => true]
+@test length(occurrences(taxon("Alces alces"), queryset...)) > 0
+
+end

GBIF/test/occurrence.jl

@@ -10,8 +10,9 @@ o = occurrence(k)
 @test o.key == k
 
 # This occurrence has been deleted, so this needs some wrapping
-k = 1258202889
-@test_throws "cannot be accessed - error code" occurrence(k)
+# It has been added back at some point
+# k = 1258202889
+# @test_throws "cannot be accessed - error code" occurrence(k)
 
 # This occurrence is incorrectly formatted for some reason
 k = 1039645472

GBIF/test/runtests.jl

@@ -12,6 +12,7 @@ tests = [
     "methods" => "methods.jl",
     "query support" => "query.jl",
     "tables interface" => "tables.jl",
+    "edge cases" => "edgecases.jl",
 ]
 
 for test in tests