Merge pull request #5 from TARGENE/fix_type_issues

add downcasting of binary arrayed fields to Int

src/fields_processing.jl

@@ -23,6 +23,16 @@ end
 
 update_with_coding!(output, coding::Missing, index, coding_to_column_indices) = nothing
 
+maybe_convert_to_int(v, ::Type{<:AbstractFloat}) =
+ convert(Vector{Int}, v) 
+
+maybe_convert_to_int(v, ::Type{<:Union{Missing, AbstractFloat}}) =
+ convert(Vector{Union{Missing, Int}}, v) 
+
+maybe_convert_to_int(v, ::Any) = v
+
+maybe_convert_to_int(v) = maybe_convert_to_int(v, eltype(v))
+
 """
  process_binary_arrayed(dataset, fields_entry)
 """
@@ -55,7 +65,7 @@ function process_binary_arrayed(dataset, fields_entry)
  # This means that a trait is declared present
  # if it is diagnosed at any of the assessment visits
  for colname in field_columns
- column = dataset[!, colname]
+ column = maybe_convert_to_int(dataset[!, colname])
  for index in eachindex(column)
  coding = getindex(column, index)
  update_with_coding!(output, coding, index, coding_to_column_indices)

test/fields_processing.jl

@@ -0,0 +1,25 @@
+module TestFieldsProcessing
+
+using DataFrames
+using Test
+using UKBMain
+
+@testset "Test misc functions" begin
+ data = DataFrame(
+ A = [1.0, missing, 2.0],
+ B = [1, missing, 2],
+ C = [1., 2., 3.]
+ )
+ intA = UKBMain.maybe_convert_to_int(data.A)
+ @test eltype(intA) === Union{Missing, Int}
+ intB = UKBMain.maybe_convert_to_int(data.B)
+ @test intB === data.B
+ intC = UKBMain.maybe_convert_to_int(data.C)
+ @test eltype(intC) === Int
+
+
+end
+
+end
+
+true

test/runtests.jl

@@ -1,4 +1,5 @@
 using Test
 
 @test include("fields_list.jl")
-@test include("datasets_extraction.jl")
+@test include("datasets_extraction.jl")
+@test include("fields_processing.jl")