Missing Hetionet Link

[HxyScotthuang]

Describe the bug

When I want to import Hetionet in PyKeen, there is a 404 error as the target URL in the source code is not functioning. Please check and update the function of Hetionet().

Source code: https://pykeen.readthedocs.io/en/stable/_modules/pykeen/datasets/hetionet.html#Hetionet

URL in source code: https://github.com/hetio/hetionet/raw/master/hetnet/tsv/hetionet-v1.0-edges.sif.gz

How to reproduce

from pykeen.datasets import Hetionet

dataset = Hetionet()

train_triples = create_triples_from_pykeen_dataset(dataset.training)

Environment

Key	Value
OS	posix
Platform	Linux
Release	5.10.147+
Time	Thu Feb 2 22:07:29 2023
Python	3.8.10
PyKEEN	1.10.0
PyKEEN Hash	UNHASHED
PyKEEN Branch
PyTorch	1.13.1+cu116
CUDA Available?	true
CUDA Version	11.6
cuDNN Version	8302

Additional information

No response

Issue Template Checks

• This is not a feature request (use a different issue template if it is)
• This is not a question (use the discussions forum instead)
• I've read the text explaining why including environment information is important and understand if I omit this information that my issue will be dismissed

[cthoyt]

Hi @HxyScotthuang , looks like @dhimmel did some reorganizing on the hetionet repo. i'll try and get to this tomorrow - it just requires changing that URL in the source code. Would be glad to accept a PR if you want to take care of this yourself!

[HxyScotthuang]

It seems that the url has changed to https://github.com/hetio/hetionet/blob/main/hetnet/tsv/hetionet-v1.0-edges.sif.gz, but substituting this throws me an BadGzipFile: Not a gzipped file (b'\n\n') Error.

[HxyScotthuang]

Please have a look, as I am not sure if this is the correct URL. Thanks!

[HxyScotthuang]

It seems that the url has changed to https://github.com/hetio/hetionet/blob/main/hetnet/tsv/hetionet-v1.0-edges.sif.gz, but substituting this throws me an BadGzipFile: Not a gzipped file (b'\n\n') Error.

Code to reproduce the error:

from pykeen.datasets.base import SingleTabbedDataset

URL = 'https://github.com/hetio/hetionet/blob/main/hetnet/tsv/hetionet-v1.0-edges.sif.gz'

class Hetionet(SingleTabbedDataset):
    def __init__(self, **kwargs):
        super().__init__(url=URL, **kwargs)

dataset = Hetionet()
print(dataset.training)

[cthoyt]

Unfortunately, the original URL did not pin to a specific version. All you need to do is swap master with v1.0.0 (the tag) so it should read:

https://github.com/hetio/hetionet/raw/v1.0.0/hetnet/tsv/hetionet-v1.0-edges.sif.gz

[cthoyt]

@HxyScotthuang it's not closed until we have a code fix in the package, sketchy patches aren't good for the future ;)

[HxyScotthuang]

Oh I see. The fix is working on my end. Thank you very much for the update!

[dhimmel]

Ah I renamed the master branch to main. I thought that old URLs would continue to work. It seems like they sort of do... https://github.com/hetio/hetionet/raw/master/hetnet/tsv/hetionet-v1.0-edges.sif.gz returns 404 but still downloads the file in my browser.

I wonder if I should make a master tag so these existing download URLs continue to work (or create a master branch, but can be confusing to have both main and master).

[mberr]

You could also consider to either make a GitHub release with a release artifact to download the data, or, maybe even better, create a persistent dump of the data in Zenodo.

[dhimmel]

There is a zenodo release, but that doesn't fix the problem. The problem is that there are links in the wild to the master branch that are now broken since we renamed that branch.

I think I will try creating a master tag.

[dhimmel]

Created a master tag. See https://github.com/hetio/hetionet/releases/tag/master. Old links should continue to work now. Let me know if otherwise.

Still not a bad idea to specify an actual versioned tag like v1.0.0 or a commit hash.

[mberr]

There is a zenodo release, but that doesn't fix the problem.

It might, at least for use within PyKEEN, fix the problem, if we change to using the zenodo URL instead of accessing github/.../raw/... URLs 🙂

[dhimmel]

The way Zenodo archived the GitHub repo is that it made a zip of the repo contents as of the v1.0.0 tag. Doesn't allow URL download access to individual files in the repo.