Error in PheKnowLator/notebooks/tutorials/entity_search.ipynb

[kangyh9659]

Hello. I'm sorry but I'm trying to run the code from the entity_search.ipynb but I got stucked by some error. The error is:

NameError: name 'processes_ancestor_path_list' is not defined

This error comes from the following code:

# examine the node's ancestors prefix = 'CHEBI' chebi6503_anc_dict = processes_ancestor_path_list(nx_ancestor_search(kg, node.copy(), prefix)) chebi6503_ancestors = format_path_ancestors(chebi6503_anc_dict, node_data_dict)

To run this code, what I only did was to git clone this PheKnowLator. Probably, I need to install some other stuff?

If you could help me how to solve this problem, I would appreciate so much.
Thank you. Have a nice day.

[callahantiff]

Thanks @kangyh9659 -- so sorry about that! It looks like two utility functions were missing from the last PR. I have added them back via PR #130. Once the tests are done running. I will merge the PR and you should be able to update your cloned version to grab these changes.

For verification, the two functions (i.e., nx_ancestor_search and processes_ancestor_path_list) were being added to kg-utils.py.

Hopefully this fixes things, but if you find other problems let me know!

Thanks for using PheKnowLator! 😄

[kangyh9659]

Thank you for fixxing it. Hope you have a wonderful weekend!

[callahantiff]

No problem, hopefully there are no other snags. Please let me know if you run into anything (apologies in advance).

I hope you have a great weekend as well!