[BUG] Example download from READEME doesn't work

[xapple]

[BUG] Example download from READEME doesn't work

[saketkc]

Thanks for the bug report. I agree we should be testing more vigorously, but rather than a bug - this is more because of changes from NCBI side.

None of the URLs work:
https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR2433794/SRR2433794.1
ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR243/SRR2433794/SRR2433794.sra

[saketkc]

PRs are always welcome.

[pabisk]

Maybe you could update the readme to reflect that this feature does not work or that this example does not work? Also could you update the tool to throw an error message that is less vague?

I had the same problem being unable to get the readme examples to work and also not just with this SRP, but with almost any other SRP I have tested.

Fails with the same error:
pysradb download -p SRP095235
pysradb srx-to-srr SRX5893229

UnboundLocalError: local variable 'exp_platform_model' referenced before assignment

Gets stuck with no error message:
pysradb download -x SRX5893229

Other commands work so the install and my connection are okay, e.g.:
pysradb download -g GSE131754

python --version
Python 3.8.10
pysradb --version
pysradb 1.3.0

I would not be surprised if the NCBI ruined the pysradb feature on their end, but it would be nice if you indicated this in the readme.

[saketkc]

Yes, I agree. Apologies for the errors. I should revise the readme and check if some of the errors are addressable with code changes.

[saketkc]

These should now be fixed with release 1.4.1