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outdated documentation and problem downloading database #128

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latimerb opened this issue Aug 13, 2021 · 1 comment
Open

outdated documentation and problem downloading database #128

latimerb opened this issue Aug 13, 2021 · 1 comment

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@latimerb
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latimerb commented Aug 13, 2021 •
edited

I'm following the documentation on this page: https://github.com/AllenInstitute/aisynphys/blob/current-release/doc/source/interactive_tools.rst

When I issue the command
python tools/synaptic_dynamics.py --db-version=full
I get

KeyError: "Unknown database version; options are: ['synphys_r1.0_2019-08-29_small.sqlite', 'synphys_r1.0_2019-08-29_medium.sqlite', 'synphys_r1.0_2019-08-29_full.sqlite', 'synphys_r1.0_small.sqlite', 'synphys_r1.0_medium.sqlite', 'synphys_r1.0_full.sqlite', 'synphys_r2.0-pre1_small.sqlite', 'synphys_r2.0-pre1_medium.sqlite', 'synphys_r2.0-pre1_full.sqlite', 'synphys_r2.0-pre2_small.sqlite', 'synphys_r2.0-pre2_medium.sqlite', 'synphys_r2.0-pre3_small.sqlite', 'synphys_r2.0-pre3_medium.sqlite', 'synphys_r2.0-pre4_small.sqlite', 'synphys_r2.0-pre4_medium.sqlite']"

Which is fine, I can just switch "full" to "synphys_r2.0-pre1_full.sqlite" for example, but this should be updated in the docs.

However, when I attempt this:
python tools/synaptic_dynamics.py --db-version=synphys_r2.0-pre1_full.sqlite
I get:

Traceback (most recent call last):
  File "/Volumes/TOSHIBA EXT/aisynphys/tools/synaptic_dynamics.py", line 5, in <module>
    from aisynphys.database import default_db as db
  File "/Volumes/TOSHIBA EXT/aisynphys/aisynphys/__init__.py", line 2, in <module>
    from . import config
  File "/Volumes/TOSHIBA EXT/aisynphys/aisynphys/config.py", line 68, in <module>
    sqlite_file = get_db_path(args.db_version)
  File "/Volumes/TOSHIBA EXT/aisynphys/aisynphys/synphys_cache.py", line 37, in get_db_path
    interactive_download(url, cache_file)
  File "/Volumes/TOSHIBA EXT/aisynphys/aisynphys/util.py", line 404, in interactive_download
    size = get_url_download_size(url)
  File "/Volumes/TOSHIBA EXT/aisynphys/aisynphys/util.py", line 386, in get_url_download_size
    file_size = int(urlopen(url).info().get('Content-Length', None))
  File "/opt/anaconda3/envs/aisynphys/lib/python3.9/urllib/request.py", line 214, in urlopen
    return opener.open(url, data, timeout)
  File "/opt/anaconda3/envs/aisynphys/lib/python3.9/urllib/request.py", line 523, in open
    response = meth(req, response)
  File "/opt/anaconda3/envs/aisynphys/lib/python3.9/urllib/request.py", line 632, in http_response
    response = self.parent.error(
  File "/opt/anaconda3/envs/aisynphys/lib/python3.9/urllib/request.py", line 561, in error
    return self._call_chain(*args)
  File "/opt/anaconda3/envs/aisynphys/lib/python3.9/urllib/request.py", line 494, in _call_chain
    result = func(*args)
  File "/opt/anaconda3/envs/aisynphys/lib/python3.9/urllib/request.py", line 641, in http_error_default
    raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 403: Forbidden

I should note that I installed the repo in my external hard drive so that may be causing this issue? If so, how do I install the package on my machine and download the full database to another location (such as my external hard drive)?
@campagnola
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campagnola commented Aug 18, 2021 via email

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@campagnola @latimerb