Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

NameError: global name 'entrezaip' is not defined when doing clinvar search #52

Open
mingoo426 opened this issue Dec 8, 2020 · 0 comments

Comments

@mingoo426
Copy link

mingoo426 commented Dec 8, 2020

Hi CharGer Team!

whenever I try to use clinvar using the -l option, I encounter this error:

charger::getClinVar
warning: ClinVar ReST search batch size given is greater than max allowed (50). Overriding to max search batch size.
Traceback (most recent call last):
  File "/home/minku/anaconda3/envs/charger/bin/charger", line 744, in <module>
    main( sys.argv[1:] )
  File "/home/minku/anaconda3/envs/charger/bin/charger", line 663, in main
    mutationTypes = mutationTypes , \
  File "/home/minku/anaconda3/envs/charger/lib/python2.7/site-packages/charger/charger.py", line 879, in getExternalData
    self.getClinVar( **kwargs )
  File "/home/minku/anaconda3/envs/charger/lib/python2.7/site-packages/charger/charger.py", line 905, in getClinVar
    self.getClinVarviaREST( **kwargs )
  File "/home/minku/anaconda3/envs/charger/lib/python2.7/site-packages/charger/charger.py", line 918, in getClinVarviaREST
    ent = entrezapi()
  File "/home/minku/anaconda3/envs/charger/lib/python2.7/site-packages/biomine/webapi/entrez/entrezapi.py", line 74, in __init__
    self.setRequestLimits()
  File "/home/minku/anaconda3/envs/charger/lib/python2.7/site-packages/biomine/webapi/entrez/entrezapi.py", line 332, in setRequestLimits
    self.setSummaryBatchSize( entrezaip.summaryBatchSize )
NameError: global name 'entrezaip' is not defined

Is entrezaip supposed to be entrezapi on line 332 and 333?

Thank you! :)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant