Scopus authentication functions inconsistely across Mac and Linux systems

[poldrack]

pybliometrics version: 3.4.0 (on both systems)

Code to reproduce the bug:

git clone https://github.com/poldrack/academicdb.git
cd academicdb
pip install .
make test

Expected behavior:

• all tests pass. This works properly on my linux system.

When the same tests are run on my mac (MacOS 13.2.1), using the same version of pybliometrics and the same API key (confirmed same contents of ~/.pybliometrics/config.ini:Authentication:APIKey) on the same home network (with no VPN or proxy set on either AFAIK, and same external IP address according to https://whatismyipaddress.com/) , I get the following:

=========================== short test summary info ============================
FAILED src/test/test_query_scopus.py::test_single_record_returned - pybliometrics.scopus.exception.Scopus401Error: The requestor is not authori...
FAILED src/test/test_researcher.py::test_get_publications - pybliometrics.scopus.exception.Scopus401Error: The requestor is not authori...
FAILED src/test/test_researcher.py::test_get_coauthors - pybliometrics.scopus.exception.Scopus401Error: The requestor is not authori...
ERROR src/test/test_converters.py::test_scopus_converter - pybliometrics.scopus.exception.Scopus401Error: The requestor is not authori...
============== 3 failed, 23 passed, 5 warnings, 1 error in 18.24s ==============
make: *** [test] Error 1

[poldrack]

Note: The tests require a MongoDB instance to be running locally...

[Michael-E-Rose]

Very strange. The only idea I have is that on Mac the API key is not loaded properly.

Could you please verify that

from pybliometrics.scopus.utils.startup import KEYS
print(KEYS)

is not empty?

[poldrack]

thanks - KEYS is not empty on the Mac:

In [1]: from pybliometrics.scopus.utils.startup import KEYS
   ...: print(KEYS)
['65...04']

and contents match those on my linux box.

[poldrack]

I also tried creating a new API key and testing that - same problem.

[poldrack]

Update: I tried running the same code within a docker container on both the Mac and the linux system. I get the same Scopus401 errors in the docker container on each of those machines using the key that still works properly within a shell on the linux system.

[poldrack]

OK, figured it out: The apparent success on my linux box was due to the fact that it was using the cached results. when I moved the original .pybliometrics directory then it failed as the other machines did. Not sure what's up with my scopus key, but at least this doesn't seem to be a pybliometrics problem so I'm closing this.

[Michael-E-Rose]

Glad you found the cause!

I should have asked earlier whether the conditions to access Scopus were the same on both machines.

This documentation might help with your software: https://pybliometrics.readthedocs.io/en/stable/access.html

[poldrack]

Thanks - I hadn't realized that the results of previous searches were cached in the .pybliometrics folder, might be worth adding a note about that to the docs.

On Sun, Apr 2, 2023 at 2:41 AM Michael E. Rose @.***> wrote:

Glad you found the cause!

I should have asked earlier whether the conditions to access Scopus were the same on both machines.

This documentation might help with your software: https://pybliometrics.readthedocs.io/en/stable/access.html

— Reply to this email directly, view it on GitHub https://github.com/pybliometrics-dev/pybliometrics/issues/283#issuecomment-1493280650, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGUVEFBYB3P42X5W2PJE2LW7FCTBANCNFSM6AAAAAAWPXPSKQ . You are receiving this because you modified the open/close state.Message ID: @.***>

-- Russell A. Poldrack Albert Ray Lang Professor of Psychology Associate Director, Stanford Data Science Director, SDS Center for Open and Reproducible Science Building 420 Stanford University Stanford, CA 94305

@. @.> http://www.poldracklab.org/

[Michael-E-Rose]

might be worth adding a note about that to the docs

Where would you expect that? Because it's described at the end of each class, in the configuration page as well as a special section in Tips .

[poldrack]

thanks, that seems fine, I just need to read better :-)

On Sun, Apr 2, 2023 at 8:10 AM Michael E. Rose @.***> wrote:

might be worth adding a note about that to the docs

Where would you expect that? Because it's described at the end of each class, in the configuration page https://pybliometrics.readthedocs.io/en/stable/configuration.html as well as a special section in Tips https://pybliometrics.readthedocs.io/en/stable/tips.html#database-updates .

— Reply to this email directly, view it on GitHub https://github.com/pybliometrics-dev/pybliometrics/issues/283#issuecomment-1493368512, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGUVEF6LY7IOVE6PAFT6ULW7GJG5ANCNFSM6AAAAAAWPXPSKQ . You are receiving this because you modified the open/close state.Message ID: @.***>

-- Russell A. Poldrack Albert Ray Lang Professor of Psychology Associate Director, Stanford Data Science Director, SDS Center for Open and Reproducible Science Building 420 Stanford University Stanford, CA 94305

@. @.> http://www.poldracklab.org/