Here is a pull request to fix issue #160 from @parthnatekar, who pointed out issues with the function dataset.download_BindingDB.
Here is an outline of the fix, which should continue working when BindingDB is updated, provided they do not change the URL format too much:
Current URL for BindingDB database is malformed and out-of-date
Replace static URL with requests and re-based parsing of BindingDB download page for current download link (regex to find file like "BindingDBAll.*?.tsv.zip")
If you run the following code using the current version of the package:
from DeepPurpose import dataset
dataset.download_BindingDB('./data/')
You will get the following error:
Beginning to download dataset...
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/jprs/Desktop/DeepPurpose/DeepPurpose/dataset.py", line 175, in download_BindingDB
saved_path = wget.download(url, path)
File "/home/jprs/Desktop/DeepPurpose/venv/lib/python3.10/site-packages/wget.py", line 526, in download
(tmpfile, headers) = ulib.urlretrieve(binurl, tmpfile, callback)
File "/usr/lib/python3.10/urllib/request.py", line 241, in urlretrieve
with contextlib.closing(urlopen(url, data)) as fp:
File "/usr/lib/python3.10/urllib/request.py", line 216, in urlopen
return opener.open(url, data, timeout)
File "/usr/lib/python3.10/urllib/request.py", line 503, in open
req = Request(fullurl, data)
File "/usr/lib/python3.10/urllib/request.py", line 322, in __init__
self.full_url = url
File "/usr/lib/python3.10/urllib/request.py", line 348, in full_url
self._parse()
File "/usr/lib/python3.10/urllib/request.py", line 377, in _parse
raise ValueError("unknown url type: %r" % self.full_url)
ValueError: unknown url type: '%20https%3A//www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?download_file=/bind/downloads/BindingDB_All_2022m7.tsv.zip'
If you install the patched version and re-run the above code, the BindingDB database will download and unzip as expected.
kexinhuang12345
commented
1 year ago
Here is a pull request to fix issue #160 from @parthnatekar, who pointed out issues with the function
dataset.download_BindingDB.Here is an outline of the fix, which should continue working when BindingDB is updated, provided they do not change the URL format too much:
If you run the following code using the current version of the package:
You will get the following error:
If you install the patched version and re-run the above code, the BindingDB database will download and unzip as expected.