handle doi requests for articles with incomplete metadata

[AshtonSBradley]

If I try something that is new or very old, I hit an error that I guess is needing to handle zero citation data as a special case?

using ShortCodes
DOI("10.1103/PhysRev.65.117")

Failed to show value:

BoundsError: attempt to access 0-element JSON3.Array{Union{}, Vector{UInt8}, Vector{UInt64}} at index [1]

throw_boundserror(::JSON3.Array{Union{}, Vector{UInt8}, Vector{UInt64}}, ::Tuple{Int64})@abstractarray.jl:703
checkbounds@abstractarray.jl:668[inlined]
getindex(::JSON3.Array{Union{}, Vector{UInt8}, Vector{UInt64}}, ::Int64)@JSON3.jl:158
var"##fetch_metadata_unmemoized"(::String)@doi.jl:68
#[email protected]:62[inlined]
get!@iddict.jl:178[inlined]
fetch_metadata@Memoize.jl:61[inlined]
var"##fetch_metadata_unmemoized"(::ShortCodes.DOI{String})@doi.jl:63
#[email protected]:62[inlined]
get!(::ShortCodes.var"#3#4"{ShortCodes.DOI{String}}, ::IdDict{Any, Any}, ::Any)@iddict.jl:178
fetch_metadata(::ShortCodes.DOI{String})@Memoize.jl:61
getproperty(::ShortCodes.DOI{String}, ::Symbol)@doi.jl:26
emph_author(::ShortCodes.DOI{String})@doi.jl:104
show(::IOContext{IOBuffer}, ::MIME{Symbol("text/html")}, ::ShortCodes.DOI{String})@doi.jl:43
show_richest(::IOContext{IOBuffer}, ::Any)@PlutoRunner.jl:1186
show_richest_withreturned@PlutoRunner.jl:1100[inlined]
format_output_default(::Any, ::Any)@PlutoRunner.jl:1000
#format_output#[email protected]:1017[inlined]
#[email protected]:909[inlined]
var"#with_io_to_logs#115"(::Bool, ::Base.CoreLogging.LogLevel, ::typeof(Main.PlutoRunner.with_io_to_logs), ::Main.PlutoRunner.var"#53#56"{Module, ShortCodes.DOI{String}, Dict{Tuple{UInt64, Int64}, Int64}})@PlutoRunner.jl:2424
(::Main.PlutoRunner.var"#119#120"{Bool, Base.CoreLogging.LogLevel, Main.PlutoRunner.var"#53#56"{Module, ShortCodes.DOI{String}, Dict{Tuple{UInt64, Int64}, Int64}}})()@PlutoRunner.jl:2448
with_logstate(::Function, ::Any)@logging.jl:511
with_logger@logging.jl:623[inlined]
#with_logger_and_io_to_logs#[email protected]:2447[inlined]
var"#formatted_result_of#50"(::Bool, ::typeof(Main.PlutoRunner.formatted_result_of), ::Base.UUID, ::Base.UUID, ::Bool, ::Vector{String}, ::Nothing, ::Module)@PlutoRunner.jl:908
top-level scope@WorkspaceManager.jl:527

DOI("10.1103/PhysRevA.107.010101")

Failed to show value:

BoundsError: attempt to access 0-element JSON3.Array{Union{}, Vector{UInt8}, Vector{UInt64}} at index [1]

throw_boundserror(::JSON3.Array{Union{}, Vector{UInt8}, Vector{UInt64}}, ::Tuple{Int64})@abstractarray.jl:703
checkbounds@abstractarray.jl:668[inlined]
getindex(::JSON3.Array{Union{}, Vector{UInt8}, Vector{UInt64}}, ::Int64)@JSON3.jl:158
var"##fetch_metadata_unmemoized"(::String)@doi.jl:68
#[email protected]:62[inlined]
get!@iddict.jl:178[inlined]
fetch_metadata@Memoize.jl:61[inlined]
var"##fetch_metadata_unmemoized"(::ShortCodes.DOI{String})@doi.jl:63
#[email protected]:62[inlined]
get!(::ShortCodes.var"#3#4"{ShortCodes.DOI{String}}, ::IdDict{Any, Any}, ::Any)@iddict.jl:178
fetch_metadata(::ShortCodes.DOI{String})@Memoize.jl:61
getproperty(::ShortCodes.DOI{String}, ::Symbol)@doi.jl:26
emph_author(::ShortCodes.DOI{String})@doi.jl:104
show(::IOContext{IOBuffer}, ::MIME{Symbol("text/html")}, ::ShortCodes.DOI{String})@doi.jl:43
show_richest(::IOContext{IOBuffer}, ::Any)@PlutoRunner.jl:1186
show_richest_withreturned@PlutoRunner.jl:1100[inlined]
format_output_default(::Any, ::Any)@PlutoRunner.jl:1000
#format_output#[email protected]:1017[inlined]
#[email protected]:909[inlined]
var"#with_io_to_logs#115"(::Bool, ::Base.CoreLogging.LogLevel, ::typeof(Main.PlutoRunner.with_io_to_logs), ::Main.PlutoRunner.var"#53#56"{Module, ShortCodes.DOI{String}, Dict{Tuple{UInt64, Int64}, Int64}})@PlutoRunner.jl:2424
(::Main.PlutoRunner.var"#119#120"{Bool, Base.CoreLogging.LogLevel, Main.PlutoRunner.var"#53#56"{Module, ShortCodes.DOI{String}, Dict{Tuple{UInt64, Int64}, Int64}}})()@PlutoRunner.jl:2448
with_logstate(::Function, ::Any)@logging.jl:511
with_logger@logging.jl:623[inlined]
#with_logger_and_io_to_logs#[email protected]:2447[inlined]
var"#formatted_result_of#50"(::Bool, ::typeof(Main.PlutoRunner.formatted_result_of), ::Base.UUID, ::Base.UUID, ::Bool, ::Vector{String}, ::Nothing, ::Module)@PlutoRunner.jl:908
top-level scope@WorkspaceManager.jl:527

[hellemo]

It's actually missing metadata that leads to this error. This is not new behaviour on ShortCodes' part, but apparently the new API has less coverage in terms of dois, so I agree it's quite annoying.

I originally figured there was no use in a fallback method for missing metadata, but willing to reconsider if there are good suggestions for what the fallback behavior should be. Just displaying the doi, perhaps?

julia> using Revise, ShortCodes

julia> ShortCodes.fetch_citation_count("10.1103/PhysRev.65.117")
4661

julia> ShortCodes.fetch_metadata("10.1103/PhysRev.65.117")
ERROR: BoundsError: attempt to access 0-element JSON3.Array{Union{}, Vector{UInt8}, Vector{UInt64}} at index [1]
Stacktrace:
 [1] throw_boundserror(A::JSON3.Array{Union{}, Vector{UInt8}, Vector{UInt64}}, I::Tuple{Int64})
   @ Base ./abstractarray.jl:745
 [2] checkbounds
   @ ./abstractarray.jl:710 [inlined]
 [3] getindex(arr::JSON3.Array{Union{}, Vector{UInt8}, Vector{UInt64}}, i::Int64)
   @ JSON3 ~/.julia/packages/JSON3/CpNms/src/JSON3.jl:158
 [4] var"##fetch_metadata_unmemoized"(doi::String)
   @ ShortCodes ~/code/ShortCodes.jl/src/doi.jl:68
 [5] #5
   @ ~/.julia/packages/Memoize/12ANR/src/Memoize.jl:62 [inlined]
 [6] get!
   @ ./iddict.jl:178 [inlined]
 [7] fetch_metadata(doi::String)
   @ ShortCodes ~/.julia/packages/Memoize/12ANR/src/Memoize.jl:61
 [8] top-level scope
   @ REPL[4]:1
julia>

[AshtonSBradley]

It's actually missing metadata that leads to this error. This is not new behaviour on ShortCodes' part, but apparently the new API has less coverage in terms of dois, so I agree it's quite annoying.

I originally figured there was no use in a fallback method for missing metadata, but willing to reconsider if there are good suggestions for what the fallback behavior should be. Just displaying the doi, perhaps?

julia> using Revise, ShortCodes

julia> ShortCodes.fetch_citation_count("10.1103/PhysRev.65.117")
4661

julia> ShortCodes.fetch_metadata("10.1103/PhysRev.65.117")
ERROR: BoundsError: attempt to access 0-element JSON3.Array{Union{}, Vector{UInt8}, Vector{UInt64}} at index [1]
Stacktrace:
 [1] throw_boundserror(A::JSON3.Array{Union{}, Vector{UInt8}, Vector{UInt64}}, I::Tuple{Int64})
   @ Base ./abstractarray.jl:745
 [2] checkbounds
   @ ./abstractarray.jl:710 [inlined]
 [3] getindex(arr::JSON3.Array{Union{}, Vector{UInt8}, Vector{UInt64}}, i::Int64)
   @ JSON3 ~/.julia/packages/JSON3/CpNms/src/JSON3.jl:158
 [4] var"##fetch_metadata_unmemoized"(doi::String)
   @ ShortCodes ~/code/ShortCodes.jl/src/doi.jl:68
 [5] #5
   @ ~/.julia/packages/Memoize/12ANR/src/Memoize.jl:62 [inlined]
 [6] get!
   @ ./iddict.jl:178 [inlined]
 [7] fetch_metadata(doi::String)
   @ ShortCodes ~/.julia/packages/Memoize/12ANR/src/Memoize.jl:61
 [8] top-level scope
   @ REPL[4]:1
julia>

I agree, if missing metadata, a good fallback would be just to show the doi link.

[AshtonSBradley]

I'm happy to have a go at this if you can suggest the right place to set the fallback from the metadata error

[stefanbringuier]

@AshtonSBradley I created a pull request (#14) that hopefully fixes this. I didn't touch the Base.show methods so the displayed result may have preceding or trailing white space after the doi link.