Command line wrapper #22
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lhannest
commented
May 1, 2018
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- Resolves command line wrapper #10
- Developed command line wrapper in kgx/kgx.py
- Changed requirements: pandas<0.21 to resolve installation error (as suggested by pip installation fails: Double requirement given: numpy==1.12.1... pandas-dev/pandas#20723)
- Added requirement: pymongo==3.6.1 to get rid of pymongo warning.
- PandasTransformer save method now saves both edge set and node set, and collects the files into a tar file. - Updated README.md to show examples from tests - Made kgx command line wrapper print the name of the directory upon success, since the output filename is not necessarily what the user requested.
cmungall
approved these changes
May 1, 2018
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Looks great!
Why is pymongo required?
https://github.com/NCATS-Tangerine/kgx/pull/22/files#diff-b4ef698db8ca845e5845c4618278f29aR11
should click not be in requirements.txt?
- Added click to requirements.txt - Fix mistaken error message in kgx.py - Fix ziptype file extention bug in pandas_transformer.py
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@cmungall I added pymongo just to get rid of the warning: Alternatively, we could |
- Now calling report method to print cardinality of edges and nodes
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ah, I guess prefixcommons i bringing in cachier, and cachier brings in mongo_core, and that has the warning. we should fix prefixcommons (our code), when we fix ontobio to go from cachier to diskcache biolink/ontobio#140 cc @deepakunni3 |
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