Added Huggingface support by ParamThakkar123 · Pull Request #13 · JuliaHealth/HealthSampleData.jl

ParamThakkar123 · 2025-10-20T13:53:14Z

This PR Fixes #12

Added a _huggingface_dataset_register to register datasets from huggingface hub using DataDeps.jl and implemented a load function to load the dataset using HealthSampleData.jl module for the users

TheCedarPrince

Thank you so much @ParamThakkar123 for your work! I left a bunch of comments based on our call; apologies for the delay in reviewing with being out sick! Very excited here and happy to review multiple times as needed. Just let me know via ping again!

I think we also will need to implement #14 first before continuing with this PR however.

Project.toml

src/huggingface.jl

test/runtests.jl

src/HealthSampleData.jl

TheCedarPrince · 2025-10-30T03:03:31Z

Hey @ParamThakkar123 , I think you are unblocked on this PR now! Could you rebase and address the comments I left here? Thanks and keep up the good work! :D

ParamThakkar123 · 2025-10-30T03:35:38Z

Hey @ParamThakkar123 , I think you are unblocked on this PR now! Could you rebase and address the comments I left here? Thanks and keep up the good work! :D

Yes @TheCedarPrince I will start working on this now!!

codecov · 2025-10-30T03:40:37Z

Codecov Report

❌ Patch coverage is 6.55738% with 57 lines in your changes missing coverage. Please review.
⚠️ Please upload report for BASE (main@921e0ee). Learn more about missing BASE report.

Files with missing lines	Patch %	Lines
src/huggingface.jl	0.00%	29 Missing ⚠️
src/HuggingFaceDatasets/data.jl	20.00%	16 Missing ⚠️
src/utilities.jl	0.00%	12 Missing ⚠️

Additional details and impacted files

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##             main     #13   +/-   ##
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TheCedarPrince

Hey Param, very very close here! Some final comments; thanks for the hard work!

Project.toml

src/HuggingFaceDatasets/data.jl

TheCedarPrince · 2025-11-07T14:24:46Z

test/runtests.jl

 using HealthSampleData
 using Test

-@testset "HealthSampleData.jl" begin


Add tests for downloading; you could upload a very small file to HF JuliaHealthDatasets and use that for testing.

Hey @ParamThakkar123 , you didn't add a test for downloading the test file. Could you do that? Additionally, please note that you can set DataDeps to always be downloaded in CI; read here: https://www.oxinabox.net/DataDeps.jl/stable/z10-for-end-users/#Configuration-1

TheCedarPrince

Hey Param, very very close here! Some final comments; thanks for the hard work!

ParamThakkar123 · 2025-11-11T11:17:18Z

@TheCedarPrince I fixed the error which was occurring during our call yesterday. The HealthSampleData.download_hf_dataset("Test") should work perfectly now. Can you please review this and also check if this works on your side too ?

TheCedarPrince · 2025-11-11T18:11:27Z

Hey @ParamThakkar123

I tried out the code and it still doesn't work. I did this and it hung indefinitely until I pressed Ctrl+C:

julia> HealthSampleData.download_hf_dataset("Test")
[ Info: Downloading Test dataset as DataDep...
[ Info: Resolving Hugging Face metadata for https://huggingface.co/datasets/JuliaHealthOrg/JuliaHealthDatasets

^C┌ Warning: Failed to resolve dataset metadata: HTTP.Exceptions.RequestError(HTTP.Messages.Request:
│ """
│ GET /api/datasets/https://huggingface.co/datasets/JuliaHealthOrg/JuliaHealthDatasets/revision/main HTTP/1.1
│ Host: huggingface.co
│ Accept: */*
│ User-Agent: HTTP.jl/1.11.7
│ Content-Length: 0
│ Accept-Encoding: gzip
│ 
│ """, InterruptException()). Falling back to direct download.
└ @ HealthSampleData ~/FOSS/HealthSampleData.jl/src/huggingface.jl:23
[ Info: Downloading penguins.csv from https://huggingface.co/datasets/JuliaHealthOrg/JuliaHealthDatasets via HuggingFaceHub...
[ Info: Downloading https://huggingface.co/datasets/JuliaHealthOrg/JuliaHealthDatasets/resolve/main/penguins.csv -> /tmp/jl_p2qTDI/penguins.csv
^CERROR: InterruptException:
Stacktrace:
 [1] open_nolock
   @ ~/.julia/juliaup/julia-1.11.7+0.x64.linux.gnu/share/julia/stdlib/v1.11/ArgTools/src/ArgTools.jl:35 [inlined]
 [2] arg_write(f::Function, arg::String)
   @ ArgTools ~/.julia/juliaup/julia-1.11.7+0.x64.linux.gnu/share/julia/stdlib/v1.11/ArgTools/src/ArgTools.jl:103
 [3] #download#2
   @ ~/.julia/juliaup/julia-1.11.7+0.x64.linux.gnu/share/julia/stdlib/v1.11/Downloads/src/Downloads.jl:258 [inlined]
 [4] download
   @ ~/.julia/juliaup/julia-1.11.7+0.x64.linux.gnu/share/julia/stdlib/v1.11/Downloads/src/Downloads.jl:247 [inlined]
 [5] _huggingface_dataset_register(name::String, repo::String, filename::String)
   @ HealthSampleData ~/FOSS/HealthSampleData.jl/src/huggingface.jl:42
 [6] Test
   @ ~/FOSS/HealthSampleData.jl/src/HuggingFaceDatasets/data.jl:33 [inlined]
 [7] download_hf_dataset(name::String)
   @ HealthSampleData ~/FOSS/HealthSampleData.jl/src/HuggingFaceDatasets/data.jl:69
 [8] top-level scope
   @ REPL[5]:1

I was looking at your code for this and it is doing a variety of weird things -- if you are using LLM-generated code here, the LLM is leading you wrong. Let me make some comments.

ParamThakkar123 · 2025-11-11T18:19:01Z

I tried this out and it worked for me. I am able to download the datasets and store it into the right place

ParamThakkar123 · 2025-11-11T18:19:09Z

Will take a look into this again

TheCedarPrince

Hey @ParamThakkar123 , I left multiple comments as we are getting close. As I pointed out, if you were using LLMs, it led you to doing a lot of strange things in the code itself. Please review my comments carefully as this corrects a lot of what the LLM was having you do.

src/HuggingFaceDatasets/data.jl

src/huggingface.jl

TheCedarPrince · 2025-11-11T18:21:32Z

src/huggingface.jl

+    try
+        # Prefer official HuggingFaceHub download if dataset info is available
+        if dataset !== nothing
+            localpath = HF.file_download(dataset, filename; progress = progress_fn)
+        else
+            # Direct fallback if HF.info failed
+            url = "$repo/resolve/main/$filename"
+            tmpdir = mktempdir()
+            dest = joinpath(tmpdir, filename)
+            @info "Downloading $url -> $dest"
+            Downloads.download(url, dest; progress = progress_fn)
+            localpath = dest
+        end
+        @info "Downloaded to $localpath"
+        return localpath
+
+    catch e
+        msg = string(e)
+        if occursin("symlink", msg) || occursin("creating symlinks", msg) ||
+           occursin("Administrator", msg) || occursin("operation not permitted", msg)
+
+            @warn "Symlink creation failed (likely Windows privilege issue). Falling back to direct HTTP download: $e"
+            url = "$repo/resolve/main/$filename"
+            tmpdir = mktempdir()
+            dest = joinpath(tmpdir, filename)
+            @info "Downloading $url -> $dest (no symlink)"
+            Downloads.download(url, dest; progress = progress_fn)
+            localpath = dest
+            @info "Fallback download complete: $localpath"
+            return localpath
+        else
+            rethrow(e)
+        end


I would instead just turn this into a simple try catch block that does:

try localpath = HF.file_download(dataset, filename) catch e @error "Dataset X had an error; please open an issue at HEALTHSAMPLEDATA-URL" end

We should be forcing it to use HuggingFaceHub and if it fails, that is an error from HF that we would need to address. The other content I really do not know what it is there for because DataDeps handles all the pathing.

The other things are for symlink errors that occured frequently with windows

src/HuggingFaceDatasets/data.jl

TheCedarPrince · 2025-11-11T18:32:58Z

test/runtests.jl

 using HealthSampleData
 using Test

-@testset "HealthSampleData.jl" begin


Hey @ParamThakkar123 , you didn't add a test for downloading the test file. Could you do that? Additionally, please note that you can set DataDeps to always be downloaded in CI; read here: https://www.oxinabox.net/DataDeps.jl/stable/z10-for-end-users/#Configuration-1

test/runtests.jl

ParamThakkar123 · 2025-11-29T08:46:24Z

Hello @TheCedarPrince , Here is a complete issue log of the issues I am facing. I have updated the PR, so it will be easy to reproduce :

The current issue is :

HuggingFaceDatasets - Test dataset download: Error During Test at E:\HealthSampleData.jl\test\runtests.jl:11
  Got exception outside of a @test
  RequestError: URL rejected: No host part in the URL while requesting /api/resolve-cache/datasets/JuliaHealthOrg/JuliaHealthDatasets/8c44aa0cf9ce035ae820fb9ec2cedfba73101435/penguins.csv?%2Fdatasets%2FJuliaHealthOrg%2FJuliaHealthDatasets%2Fresolve%2F8c44aa0cf9ce035ae820fb9ec2cedfba73101435%2Fpenguins.csv=&etag=%2225b46d384bf81f8399188500ea54917bb49d8890%22
  Stacktrace:
    [1] (::Downloads.var"#23#24"{IOStream, Base.DevNull, String, Vector{Any}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool})(easy::Downloads.Curl.Easy)
      @ Downloads E:\Julia-1.12.1\share\julia\stdlib\v1.12\Downloads\src\Downloads.jl:452
    [2] with_handle(f::Downloads.var"#23#24"{IOStream, Base.DevNull, String, Vector{Any}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool}, handle::Downloads.Curl.Easy)
      @ Downloads.Curl E:\Julia-1.12.1\share\julia\stdlib\v1.12\Downloads\src\Curl\Curl.jl:105
    [3] #21
      @ E:\Julia-1.12.1\share\julia\stdlib\v1.12\Downloads\src\Downloads.jl:363 [inlined]
    [4] arg_write(f::Downloads.var"#21#22"{Base.DevNull, String, Vector{Any}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool}, arg::IOStream)
      @ ArgTools E:\Julia-1.12.1\share\julia\stdlib\v1.12\ArgTools\src\ArgTools.jl:134
    [5] #19
      @ E:\Julia-1.12.1\share\julia\stdlib\v1.12\Downloads\src\Downloads.jl:362 [inlined]
    [6] arg_read
      @ E:\Julia-1.12.1\share\julia\stdlib\v1.12\ArgTools\src\ArgTools.jl:76 [inlined]
    [7] request(url::String; input::Nothing, output::IOStream, method::String, headers::Vector{Any}, timeout::Float64, progress::Nothing, verbose::Bool, debug::Nothing, throw::Bool, downloader::Nothing, interrupt::Nothing)
      @ Downloads E:\Julia-1.12.1\share\julia\stdlib\v1.12\Downloads\src\Downloads.jl:361
    [8] request
      @ E:\Julia-1.12.1\share\julia\stdlib\v1.12\Downloads\src\Downloads.jl:328 [inlined]
    [9] #4
      @ E:\Julia-1.12.1\share\julia\stdlib\v1.12\Downloads\src\Downloads.jl:259 [inlined]
   [10] open(f::Downloads.var"#4#5"{String, Vector{Any}, Float64, Nothing, Bool, Nothing, Nothing, String}, args::String; kwargs::@Kwargs{write::Bool, lock::Bool})
      @ Base .\io.jl:410
   [11] open_nolock
      @ E:\Julia-1.12.1\share\julia\stdlib\v1.12\ArgTools\src\ArgTools.jl:35 [inlined]
   [12] arg_write(f::Function, arg::String)
      @ ArgTools E:\Julia-1.12.1\share\julia\stdlib\v1.12\ArgTools\src\ArgTools.jl:103
   [13] #download#2
      @ E:\Julia-1.12.1\share\julia\stdlib\v1.12\Downloads\src\Downloads.jl:258 [inlined]
   [14] download
      @ E:\Julia-1.12.1\share\julia\stdlib\v1.12\Downloads\src\Downloads.jl:247 [inlined]
   [15] file_download(repo::HuggingFaceHub.Dataset, path::String; client::HuggingFaceHub.Client, progress::Nothing)
      @ HuggingFaceHub C:\Users\Hp\.julia\packages\HuggingFaceHub\dgGqM\src\files.jl:153
   [16] file_download
      @ C:\Users\Hp\.julia\packages\HuggingFaceHub\dgGqM\src\files.jl:53 [inlined]
   [17] _huggingface_dataset_register(name::String, repo::String, filename::String)
      @ HealthSampleData E:\HealthSampleData.jl\src\huggingface.jl:22
   [18] Test()
      @ HealthSampleData E:\HealthSampleData.jl\src\HuggingFaceDatasets\data.jl:21
   [19] download_hf_dataset(name::String)
      @ HealthSampleData E:\HealthSampleData.jl\src\HuggingFaceDatasets\data.jl:57
   [20] top-level scope
      @ E:\HealthSampleData.jl\test\runtests.jl:5
   [21] macro expansion
      @ E:\Julia-1.12.1\share\julia\stdlib\v1.12\Test\src\Test.jl:1776 [inlined]
   [22] macro expansion
      @ E:\HealthSampleData.jl\test\runtests.jl:12 [inlined]
   [23] macro expansion
      @ E:\Julia-1.12.1\share\julia\stdlib\v1.12\Test\src\Test.jl:1776 [inlined]
   [24] macro expansion
      @ E:\HealthSampleData.jl\test\runtests.jl:12 [inlined]
   [25] include(mapexpr::Function, mod::Module, _path::String)
      @ Base .\Base.jl:307
   [26] top-level scope
      @ none:6
   [27] eval(m::Module, e::Any)
      @ Core .\boot.jl:489
   [28] exec_options(opts::Base.JLOptions)
      @ Base .\client.jl:283
   [29] _start()
      @ Base .\client.jl:550
Test Summary:                                 | Pass  Error  Total  Time
HealthSampleData.jl                           |    4      1      5  6.1s
  HuggingFaceDatasets - Test dataset download |           1      1  4.4s
RNG of the outermost testset: Random.Xoshiro(0xee5a5de7590e9b2d, 0x744e9f964adc9fa0, 0xe20203f4ea99eee6, 0x17fdee9386999f4b, 0x5d41d67b7cd97f98)
ERROR: LoadError: Some tests did not pass: 4 passed, 0 failed, 1 errored, 0 broken.
in expression starting at E:\HealthSampleData.jl\test\runtests.jl:4
ERROR: Package HealthSampleData errored during testing

Added Huggingface support

896d63c

ParamThakkar123 requested a review from TheCedarPrince October 20, 2025 13:53

TheCedarPrince requested changes Oct 24, 2025

View reviewed changes

Rebase

96bf072

Updates as per review

36cdc84

ParamThakkar123 requested a review from TheCedarPrince November 1, 2025 03:34

TheCedarPrince requested changes Nov 7, 2025

View reviewed changes

ParamThakkar123 and others added 8 commits November 10, 2025 20:43

Begin writing documentation

5e3e5de

First draft of HuggingFace downloading

cc52ddf

First draft of tests

525541b

Back up for Param's HF branch

47807d2

First draft at making quick start guide

3acfe4d

Added Changes to huggingface.jl files

23d0566

Modified Project.toml

5950233

Added fix for download failures

4802009

ParamThakkar123 requested a review from TheCedarPrince November 11, 2025 11:17

TheCedarPrince requested changes Nov 11, 2025

View reviewed changes

ParamThakkar123 added 5 commits November 12, 2025 00:11

Removed tests for progress callback

9047a36

Simplified dataset logic to HF.info

5a66f41

Added some fixes

e5d8648

removed progress callback

c1707c5

removed utilities file

e8523d3

ParamThakkar123 added 5 commits November 14, 2025 19:02

Removed hf register export

8150afe

removed unused file

7d2ab9d

added tests for Test file

6b0b299

Added environment to always download datadeps in CI

29f9528

revised the fetch_method

3ed1afd

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