Cannot download human dataset

[guillermoturiel]

Hello,

Thank you very much for developing this software. Seems quite interesting and I am looking forward to try it on my data.

I have been following the full-example.ipynb document but I have encountered an error that blocks my progress.

When running sn.download.db() I get the following error:

In [113]: sn.download_db()
Do you want to install datasets for (human/mouse/both)?
human
human.zip: 0.00B [00:03, ?B/s]

HTTPError Traceback (most recent call last)
Cell In[113], line 1
----> 1 sn.download_db()

File ~/anaconda3/envs/scanet/lib/python3.9/site-packages/scanet/download_db.py:41, in download_db()
39 filename_ = os.path.join(MAIN_PATH, "databases",os.path.basename(dataset_human))
40 with DownloadProgressBar(unit='B', unit_scale=True, miniters=1, desc=dataset_human.split('/')[-1]) as t:
---> 41 request.urlretrieve(dataset_human, filename=filename_,
42 reporthook=t.update_to)
45 if answer == "mouse" or answer == "both":
46 if db_exists("mouse"):

File ~/anaconda3/envs/scanet/lib/python3.9/urllib/request.py:239, in urlretrieve(url, filename, reporthook, data)
222 """
223 Retrieve a URL into a temporary location on disk.
224
(...)
235 data file as well as the resulting HTTPMessage object.
236 """
237 url_type, path = _splittype(url)
--> 239 with contextlib.closing(urlopen(url, data)) as fp:
240 headers = fp.info()
242 # Just return the local path and the "headers" for file://
243 # URLs. No sense in performing a copy unless requested.

File ~/anaconda3/envs/scanet/lib/python3.9/urllib/request.py:214, in urlopen(url, data, timeout, cafile, capath, cadefault, context)
212 else:
213 opener = _opener
--> 214 return opener.open(url, data, timeout)

File ~/anaconda3/envs/scanet/lib/python3.9/urllib/request.py:523, in OpenerDirector.open(self, fullurl, data, timeout)
521 for processor in self.process_response.get(protocol, []):
522 meth = getattr(processor, meth_name)
--> 523 response = meth(req, response)
525 return response

File ~/anaconda3/envs/scanet/lib/python3.9/urllib/request.py:632, in HTTPErrorProcessor.http_response(self, request, response)
629 # According to RFC 2616, "2xx" code indicates that the client's
630 # request was successfully received, understood, and accepted.
631 if not (200 <= code < 300):
--> 632 response = self.parent.error(
633 'http', request, response, code, msg, hdrs)
635 return response

File ~/anaconda3/envs/scanet/lib/python3.9/urllib/request.py:561, in OpenerDirector.error(self, proto, *args)
559 if http_err:
560 args = (dict, 'default', 'http_error_default') + orig_args
--> 561 return self._call_chain(*args)

File ~/anaconda3/envs/scanet/lib/python3.9/urllib/request.py:494, in OpenerDirector._call_chain(self, chain, kind, meth_name, *args)
492 for handler in handlers:
493 func = getattr(handler, meth_name)
--> 494 result = func(*args)
495 if result is not None:
496 return result

File ~/anaconda3/envs/scanet/lib/python3.9/urllib/request.py:641, in HTTPDefaultErrorHandler.http_error_default(self, req, fp, code, msg, hdrs)
640 def http_error_default(self, req, fp, code, msg, hdrs):
--> 641 raise HTTPError(req.full_url, code, msg, hdrs, fp)

HTTPError: HTTP Error 404: Not Found

When looking into download_db.py I see that there are two links for the human and mouse datasets:

dataset_human = "https://wolken.zbh.uni-hamburg.de/index.php/s/DZ3XT76Z7xYAT64/download/human.zip"
dataset_mouse = "https://wolken.zbh.uni-hamburg.de/index.php/s/6syqpRTgDLaQs4t/download/mouse.zip"

I suspect that the problem is here, when trying to download the data from this link. I think there is some kind of access problem as this is what I see when trying to open the link in a normal browser:

Could you please provide some help to solve this? Or maybe an alternative way of downloading the dataset?

Thank very much

Best
Guillermo

[oubounyt]

Hello Guillermo,

Thank you for your kind words and your interest in the software. I apologize for the inconvenience you're facing with the dataset download. I appreciate your patience.

I've identified the issue and am working on resolving it. In the meantime, here are the new links to download the human and mouse datasets:

Human Dataset: https://cloud.uni-hamburg.de/s/YCJkWqebaP5poLH
Mouse Dataset: https://cloud.uni-hamburg.de/s/8ndzG5fm77e6dPG

I will also include these updated links in the upcoming version. If you encounter any further issues or have additional questions, please don't hesitate to reach out.