Some TU Datasets do not work - Error when loading

[chrisn-pik]

Unfortunately, some TU Datasets can not be loaded. The following example illustrates the problem for dataset "Cuneiform":

using MLDatasets
tudata = TUDataset("Cuneiform")

The following error message occurs:

ERROR: at row 1, column 1 : ErrorException("file entry \"0,\" cannot be converted to Int64")
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] dlm_fill(T::DataType, offarr::Vector{Vector{Int64}}, dims::Tuple{Int64, Int64}, has_header::Bool, sbuff::String, auto::Bool, eol::Char)
    @ DelimitedFiles /usr/share/julia/stdlib/v1.8/DelimitedFiles/src/DelimitedFiles.jl:515
  [3] readdlm_string(sbuff::String, dlm::Char, T::Type, eol::Char, auto::Bool, optsd::Dict{Symbol, Union{Char, Integer, Tuple{Integer, Integer}}})
    @ DelimitedFiles /usr/share/julia/stdlib/v1.8/DelimitedFiles/src/DelimitedFiles.jl:471
  [4] readdlm_auto(input::String, dlm::Char, T::Type, eol::Char, auto::Bool; opts::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ DelimitedFiles /usr/share/julia/stdlib/v1.8/DelimitedFiles/src/DelimitedFiles.jl:247
  [5] readdlm_auto
    @ /usr/share/julia/stdlib/v1.8/DelimitedFiles/src/DelimitedFiles.jl:233 [inlined]
  [6] #readdlm#6
    @ /usr/share/julia/stdlib/v1.8/DelimitedFiles/src/DelimitedFiles.jl:226 [inlined]
  [7] readdlm
    @ /usr/share/julia/stdlib/v1.8/DelimitedFiles/src/DelimitedFiles.jl:226 [inlined]
  [8] #readdlm#1
    @ /usr/share/julia/stdlib/v1.8/DelimitedFiles/src/DelimitedFiles.jl:57 [inlined]
  [9] readdlm
    @ /usr/share/julia/stdlib/v1.8/DelimitedFiles/src/DelimitedFiles.jl:57 [inlined]
 [10] TUDataset(name::String; dir::Nothing)
    @ MLDatasets ~/.julia/packages/MLDatasets/OYCcg/src/datasets/graphs/tudataset.jl:74
 [11] TUDataset(name::String)
    @ MLDatasets ~/.julia/packages/MLDatasets/OYCcg/src/datasets/graphs/tudataset.jl:54

caused by: file entry "0," cannot be converted to Int64
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] store_cell(dlmstore::DelimitedFiles.DLMStore{Int64}, row::Int64, col::Int64, quoted::Bool, startpos::Int64, endpos::Int64)
    @ DelimitedFiles /usr/share/julia/stdlib/v1.8/DelimitedFiles/src/DelimitedFiles.jl:388
  [3] dlm_fill(T::DataType, offarr::Vector{Vector{Int64}}, dims::Tuple{Int64, Int64}, has_header::Bool, sbuff::String, auto::Bool, eol::Char)
    @ DelimitedFiles /usr/share/julia/stdlib/v1.8/DelimitedFiles/src/DelimitedFiles.jl:510
  [4] readdlm_string(sbuff::String, dlm::Char, T::Type, eol::Char, auto::Bool, optsd::Dict{Symbol, Union{Char, Integer, Tuple{Integer, Integer}}})
    @ DelimitedFiles /usr/share/julia/stdlib/v1.8/DelimitedFiles/src/DelimitedFiles.jl:471
  [5] readdlm_auto(input::String, dlm::Char, T::Type, eol::Char, auto::Bool; opts::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ DelimitedFiles /usr/share/julia/stdlib/v1.8/DelimitedFiles/src/DelimitedFiles.jl:247
  [6] readdlm_auto
    @ /usr/share/julia/stdlib/v1.8/DelimitedFiles/src/DelimitedFiles.jl:233 [inlined]
  [7] #readdlm#6
    @ /usr/share/julia/stdlib/v1.8/DelimitedFiles/src/DelimitedFiles.jl:226 [inlined]
  [8] readdlm
    @ /usr/share/julia/stdlib/v1.8/DelimitedFiles/src/DelimitedFiles.jl:226 [inlined]
  [9] #readdlm#1
    @ /usr/share/julia/stdlib/v1.8/DelimitedFiles/src/DelimitedFiles.jl:57 [inlined]
 [10] readdlm
    @ /usr/share/julia/stdlib/v1.8/DelimitedFiles/src/DelimitedFiles.jl:57 [inlined]
 [11] TUDataset(name::String; dir::Nothing)
    @ MLDatasets ~/.julia/packages/MLDatasets/OYCcg/src/datasets/graphs/tudataset.jl:74
 [12] TUDataset(name::String)
    @ MLDatasets ~/.julia/packages/MLDatasets/OYCcg/src/datasets/graphs/tudataset.jl:54
  

Other problems arise for Fingerprint:

tudata = TUDataset("Fingerprint")

AssertionError: all(sort(unique(graph_indicator)) .== 1:length(unique(graph_indicator)))
Stacktrace:
 [1] TUDataset(name::String; dir::Nothing)
   @ MLDatasets ~/.julia/packages/MLDatasets/OYCcg/src/datasets/graphs/tudataset.jl:66
 [2] TUDataset(name::String)
   @ MLDatasets ~/.julia/packages/MLDatasets/OYCcg/src/datasets/graphs/tudataset.jl:54
 [3] top-level scope
   @ REPL[5]:1

[Dsantra92]

Thanks @chrisn-pik for reporting this!!

[CarloLucibello]

@chrisn-pik can you confirm that everything works on last tagged version?

[chrisn-pik]

@CarloLucibello Thanks for the quick fix. I do not get an error message in case of Cuneiform now, however, I still can not use Fingerprint, see #195 (comment).

[Dsantra92]

In our code, we expect graph labels to be numbered serially. Seems like it is not the case and is not specified in the format. Will be making a pr shortly.

[Dsantra92]

Looks like there must be some discrepancy in this particular dataset.

using DelimitedFiles: readdlm
readdlm("~/.julia/datadeps/TUDataset/Fingerprint/Fingerprint_graph_indicator.txt", Int) |> unique |> length

gives 2149. Which means there are 2149 graphs with nodes. But the original docs and other files like graph_labels.txt say it's 2800. The error in loading the dataset is to be expected.

Removing the check and changing a few lines can load the data, but should we?
cc: @CarloLucibello

[CarloLucibello]

we can turn the error into a warning