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saketkc / pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO
https://saketkc.github.io/pysradb
BSD 3-Clause "New" or "Revised" License
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pysradb download doesn't work[BUG] #155

Closed mzavolan closed 2 years ago

mzavolan commented 2 years ago

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 :

saketkc commented 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.

mzavolan commented 2 years ago

Thanks @saketkc for the fast answer. Any indication of the time frame when you would be able to look at the issue?

saketkc commented 2 years ago

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.