[BUG] KeyError: 'EXPERIMENT_PACKAGE_SET'

[Maarten-vd-Sande]

Describe the bug
version 0.11.1-dev0

import pysradb

db = pysradb.SRAweb()
db.sra_metadata("SRP098789", detailed=True)

Traceback (most recent call last):
  File "script", line 4, in <module>
    db.sra_metadata("SRP098789", detailed=True)
  File "/home/maarten/anaconda3/envs/seq2science/lib/python3.7/site-packages/pysradb/sraweb.py", line 456, in sra_metadata
    efetch_result = self.get_efetch_response("sra", srp)
  File "/home/maarten/anaconda3/envs/seq2science/lib/python3.7/site-packages/pysradb/sraweb.py", line 323, in get_efetch_response
    response = xmltodict.parse(request_text)["EXPERIMENT_PACKAGE_SET"][
KeyError: 'EXPERIMENT_PACKAGE_SET'

[Maarten-vd-Sande]

I am also pretty sure that today I got KeyError: 'EXPERIMENT_PACKAGE' before (the key one line farther), but I guess that's related to this one

[Maarten-vd-Sande]

A call to efetch gave me this result, so it seems like ncbi is down-ish. Would be nice if pysradb catches this more "gracefully", but that's a minor detail.

500 Internal Server Error

No do_post output returned from 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=sra&query_key=1&WebEnv=MCID_5f6236a16761b17fe3514db7&rettype=&retmode=text&retstart=0&retmax=1&edirect_os=linux&edirect=11.0&tool=edirect&email=jenkins@ocimum'

I think I can close this as it seems something goes wrong at ncbi side?

[saketkc]

Thanks @Maarten-vd-Sande, this indeed is arising from NCBI (I was unable to replicate it locally just now). #69 should hopefully throw out better failure messages.

[Maarten-vd-Sande]

Awesome! Thanks for these fast fixes and replies ⚡ !