JSON object must be str, not 'bytes'

[ncbi]

JSON object must be str, not 'bytes'

[azat-badretdin]

Thank you for your report. Someone will look at it soon.

[nclaesnacw]

Thanks, probably not directly a pgap issue 🙁 but hoped you would understand what's happening.

…

________________________________ From: Azat Badretdin <[email protected]> Sent: Monday, December 9, 2019 12:35:05 PM To: ncbi/pgap <[email protected]> Cc: Alan Claude Ward <[email protected]>; Author <[email protected]> Subject: Re: [ncbi/pgap] JSON object must be str, not 'bytes' (#52) Thank you for your report. Someone will look at it soon. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#52?email_source=notifications&email_token=ADR7VF3W5GS6SJN2BAECOHTQXY3PTA5CNFSM4JYIIN4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGJAODI#issuecomment-563218189>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ADR7VF5D73UX2PBGJP7NGDLQXY3PTANCNFSM4JYIIN4A>.

[azat-badretdin]

We want our software to tolerate as much variability in user system setup as possible and we are actively working on it, so your report is very useful. I am trying to investigate it right now on our setup box.

Meanwhile, a question: did you have more output from ./pgap.py --update? If yes, would you mind posting it as attachment? Thanks!

[nclaesnacw]

Hi
No - I note from pgap.py that the min python version is 3.5. But I get the json string error when I tried to run with python 2,7, before it checked the python version. We are running Ubuntu 16.04 because we are doing nanopore sequencing and the guppy basecaller from nanopore requires 16.04 - and that leaves us with default python 2,7 :-( but the python3 command should deal with that?

[azat-badretdin]

The script refers to python3 in shebang (first, #! line of the script), so any python2-related considerations are not expected to affect the outcome.

[slottad]

Sorry about that. The python version check should be the first error message you see. We'll try and get that fixed. We are mandated to move to Python 3 by our organization because Python 2 will no longer be supported. See https://www.python.org/dev/peps/pep-0373/

[nclaesnacw]

Sorry user was not in docker group!!! I was told docker was set up but didn't test :-(
Not sure how that translated into the json error
You were right /bin/usr/env python 3 at !# sets up to use the installed python 3.5 so v.2.7 not the issue
Thanks, it needs a listener sometimes

[azat-badretdin]

Feel free to test pgap.py again after you fixed the docker/user issue. I am not sure how this might have translated into the json error either.

[azat-badretdin]

We were able to reproduce the problem on one of our systems and fix it (thanks, @evolarjun)

See 2529fb0

Feel free to apply the fix locally to your pgap.py script or wait until this commit percolates in official way.