Improve errors for invalid (meta) data formats

meringlab · Oct 26, 2020 · 087cbfb · 087cbfb
1 parent 0bcae28
commit 087cbfb
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Showing 2 changed files with 16 additions and 4 deletions.
diff --git a/src/io.jl b/src/io.jl
@@ -3,9 +3,10 @@
 
 const valid_net_formats = (".edgelist", ".gml", ".jld2")
 const valid_data_formats = (".tsv", ".csv", ".biom", ".jld2")
+const valid_dlm_formats = (".tsv", ".csv")
 
 isjld(ext::AbstractString) = ext == ".jld2"
-isdlm(ext::AbstractString) = ext in (".tsv", ".csv")
+isdlm(ext::AbstractString) = ext in valid_dlm_formats
 isbiom(ext::AbstractString) = ext == ".biom"
 isedgelist(ext::AbstractString) = ext == ".edgelist"
 isgml(ext::AbstractString) = ext == ".gml"
@@ -25,21 +26,27 @@ Load matrices with OTU count and optionally meta data from disc. Available forma
 
 - `transposed` - if `true`, rows of `data` are variables and columns are samples
 """
-function load_data(data_path::AbstractString, meta_path=nothing; transposed::Bool=false,
-     otu_data_key::AbstractString="otu_data", meta_data_key="meta_data",
-     otu_header_key::AbstractString="otu_header", meta_header_key="meta_header")
+function load_data(data_path::AbstractString, meta_path::Union{AbstractString,Nothing}=nothing; transposed::Bool=false,
+     otu_data_key::AbstractString="otu_data", meta_data_key::AbstractString="meta_data",
+     otu_header_key::AbstractString="otu_header", meta_header_key::AbstractString="meta_header")
      """Load OTU tables and meta data from various formats.
      -- Set jld2 keys you don't want to use to 'nothing'
      -- delimited formats must have headers (or row indices if transposed=true)"""
     file_ext = splitext(data_path)[2]
     transposed && file_ext == ".biom" && @warn("'transposed' cannot be used with .biom files")
 
+    if meta_path != nothing
+        meta_file_ext = splitext(meta_path)[2]
+        !isdlm(meta_file_ext) && @error "$(meta_file_ext) is an invalid meta data format, please provide one of $(valid_dlm_formats)"
+    end
+
     if isdlm(file_ext)
         ld_results = load_dlm(data_path, meta_path, transposed=transposed)
     elseif isbiom(file_ext)
         ld_results = load_biom(data_path, meta_path)
     elseif isjld(file_ext)
         @warn "jld2 support is deprecated and will be removed in future versions of FlashWeave"
+        meta_path != nothing && @error "jld2 format not compatible with external meta data files, please add meta data directly to the jld2 file (default group key: 'meta_data')"
         ld_results = load_jld(data_path, otu_data_key, otu_header_key, meta_data_key, meta_header_key, transposed=transposed)
     else
         error("$(file_ext) not a valid output format. Choose one of $(valid_data_formats)")

diff --git a/test/io.jl b/test/io.jl
@@ -90,6 +90,7 @@ meta_header_fact = meta_header_fact[:]
 
         @testset "$data_format" begin
             data_path, meta_path = [joinpath("data", "HMP_SRA_gut", "HMP_SRA_gut_tiny" * suff) for suff in [data_suff, meta_suff]]
+            meta_path = isempty(meta_suff) ? nothing : meta_path
             data_ld = load_data(data_path, meta_path, meta_data_key=meta_data_key, meta_header_key=meta_header_key)
             @test data_ld[1] == data
             @test data_ld[2] == header
@@ -106,8 +107,12 @@ end
     for (data_format, data_suff, meta_suff) in zip(["tsv", "jld2"],
                                                    ["_ids_transposed.tsv", "_plus_meta_transposed.jld2"],
                                                    ["_meta_transposed.tsv", ""])
+       # skip jld2
+       data_format == "jld2" && continue
+
         @testset "$data_format" begin
             data_path, meta_path = [joinpath("data", "HMP_SRA_gut", "HMP_SRA_gut_tiny" * suff) for suff in [data_suff, meta_suff]]
+            meta_path = isempty(meta_suff) ? nothing : meta_path
             data_ld = load_data(data_path, meta_path, transposed=true, meta_data_key=meta_data_key,
                                 meta_header_key=meta_header_key)
             @test data_ld[1] == data