Unable to run chapter05 (and probably others) as unable to download pdbbind_v2015.tar.gz

[ellagale]

Running deepchem 2.3.0 in a conda environment on ubuntu.

From looking at the error by hand, it seems the url http://deepchem.io.s3-website-us-west-1.amazonaws.com/datasets/pdbbind_v2015.tar.gz is 403ing.

Stack Trace

$ python3 pdbbind_nn.py
Traceback (most recent call last):
  File "pdbbind_nn.py", line 4, in <module>
    pdbbind_tasks, pdbbind_datasets, transformers = dc.molnet.load_pdbbind(featurizer="grid", split="random", subset="core")
  File "/home/ella/anaconda3/envs/deepchem/lib/python3.7/site-packages/deepchem/molnet/load_function/pdbbind_datasets.py", line 230, in load_pdbbind
    dest_dir=data_dir)
  File "/home/ella/anaconda3/envs/deepchem/lib/python3.7/site-packages/deepchem/utils/__init__.py", line 83, in download_url
    urlretrieve(url, os.path.join(dest_dir, name))
  File "/home/ella/anaconda3/envs/deepchem/lib/python3.7/urllib/request.py", line 247, in urlretrieve
    with contextlib.closing(urlopen(url, data)) as fp:
  File "/home/ella/anaconda3/envs/deepchem/lib/python3.7/urllib/request.py", line 222, in urlopen
    return opener.open(url, data, timeout)
  File "/home/ella/anaconda3/envs/deepchem/lib/python3.7/urllib/request.py", line 531, in open
    response = meth(req, response)
  File "/home/ella/anaconda3/envs/deepchem/lib/python3.7/urllib/request.py", line 641, in http_response
    'http', request, response, code, msg, hdrs)
  File "/home/ella/anaconda3/envs/deepchem/lib/python3.7/urllib/request.py", line 569, in error
    return self._call_chain(*args)
  File "/home/ella/anaconda3/envs/deepchem/lib/python3.7/urllib/request.py", line 503, in _call_chain
    result = func(*args)
  File "/home/ella/anaconda3/envs/deepchem/lib/python3.7/urllib/request.py", line 649, in http_error_default
    raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 403: Forbidden

[ellagale]

I attempted this both from my home PC and routed via my university VPN, so I don't think it is my connection.

[rbharath]

Ah our apologies! This is because we had to switch AWS backends (our support from Stanford ran out so we swapped to our own backend). The old URLs are no longer accessible

Easiest fix here is probably to upgrade to the nightly deepchem build which points to the correct new S3 buckets with

pip install --pre deepchem

As a warning, the rest of the book code hasn't been converted to the nightly build, so there may be different errors, but we plan to make this conversion over the coming weeks as part of our upcoming release