add get method for whole community, and default for default (#120)

EcoJulia · Dec 7, 2021 · a0976b6 · a0976b6
1 parent ff40b24
commit a0976b6
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Showing 3 changed files with 12 additions and 2 deletions.
diff --git a/src/profiles.jl b/src/profiles.jl
@@ -530,7 +530,14 @@ Base.haskey(commp::CommunityProfile, sample::AbstractString, key::Symbol) = in(k
 
 Return the value of the metadata in a `sample` stored for the given `key`, or the given `default` value if no mapping for the key is present.
 """
-Base.get(commp::CommunityProfile, sample::AbstractString, key::Symbol, default) = get(metadata(samples(commp, sample)), key, default)
+Base.get(commp::CommunityProfile, sample::AbstractString, key::Symbol, default=missing) = get(metadata(samples(commp, sample)), key, default)
+
+"""
+    get(commp::CommunityProfile, key::Symbol, default)
+
+Return the value of the metadata in a `sample` stored for the given `key`, or the given `default` value if no mapping for the key is present.
+"""
+Base.get(commp::CommunityProfile, key::Symbol, default=missing) = [get(commp, sample, key, default) for sample in samplenames(commp)]
 
 
 """

diff --git a/test/MicrobiomeTests.jl b/test/MicrobiomeTests.jl
@@ -239,6 +239,7 @@ end
             @test delete!(c4, "sample1", :something) isa MicrobiomeSample
             @test !haskey(c4, "sample1", :something)
             @test get(c4, "sample1", :something_else, 42) == 42
+            @test ismissing(get(c4, "sample1", :something_else))
             @test insert!(c4, "sample1", :something, 3.0) isa MicrobiomeSample
             @test get(c4, "sample1", :something, 42) == 3.0
             set!(c4, "sample1", :something, 1.0)
@@ -275,6 +276,8 @@ end
                 insert!(c5, "sample2", (; graw="gnaw", biff="boof"))
                 @test_throws IndexError insert!(c5, [(;sample="sample1", still_other="yes"), (;sample="sample2", still_other="no")])
                 @test !haskey(c5, "sample1", :still_other)
+                @test all(get(c5, :something) .=== [1.0, missing])
+                @test all(get(c5, :something, 42.0) .== [1.0, 42.0])
             end
 
             @testset "set!" begin

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -2,4 +2,4 @@ include("MicrobiomeTests.jl")
 MicrobiomeTests.runtests()
 
 using Microbiome
-Microbiome.runtests()
+Microbiome.runtests()