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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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Json decode error (too many inputs) #138

Closed Maarten-vd-Sande closed 1 year ago

Maarten-vd-Sande commented 3 years ago

Should solve #78, as per the suggestion of @kpj. Requests simply get split up into smaller parts of 150, logic for the rest is untouched. @saketkc would this be something you are willing to support? It seems to work for me. There are a couple of cases that I am not sure about how to deal with, i put comments for those.

Unrelated, but not sure if I remember correctly so I put it here before I make an issue: I saw a couple weeks ago that ENA changed their API, and all the ena_fastq_http links are nan even for ERR accessions from pysradb.

saketkc commented 3 years ago

Thanks for the PR @Maarten-vd-Sande! I will pass it through some quick tests and also check what is going on with ENA links - thanks for bringing it to my attention

saketkc commented 2 years ago

Sorry for not being able to catch up with this @Maarten-vd-Sande. I am not quite sure why the tests fail, I will try to take a look at it this week.

Maarten-vd-Sande commented 2 years ago

No problem @saketkc! I'm guessing I messed up the indentation somewhere. If I have time somewhere coming week(s) I'll try to take a look at it as well

saketkc commented 1 year ago

Closing because of conflicts with the current master. We can reopen if there is still interest.