Closed mzavolan closed 2 years ago
Sorry, I am aware that one of the recent commits broke this functionality. I will try to have a fix soon. Apologies.
Thanks @saketkc for the fast answer. Any indication of the time frame when you would be able to look at the issue?
this has been fixed on the main branch. However the notebook example no longer works (because all the files have been moved to s3). Here's an alternate example:
$ pysradb download -p SRP312633
I will close this now, feel free to reopen if there are any other issues.
Description I am trying to run the example mentioned in the documentation, but it does not work. The first message I get is:
The supplied url column "None" cannot be found.
Then I list of urls is produced that looks like this:
run_accession study_accession experiment_accession recommended_url
SRR057533 SRP002605 SRX021977 https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR057533/SRR057533.2 ...
and I am asked
Use recommended_url instead? [Y/n]:
I choose y and I end up getting the following type of errors:
Checking download URLs Key error for: https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR057533/SRR057533.2 ...
What I did
pysradb download -p SRP002605
Using additionally the -y option gives the same error.
Desktop :