update GDC to CCDH conversion.ipynb

cancerDHC / example-data

This repository is intended to act as a store of example data files from across the NCI Cancer Research Data Commons (CRDC) nodes in a number of formats.

MIT License

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update GDC to CCDH conversion.ipynb #13

Closed turbomam closed 2 years ago

turbomam commented 3 years ago

GDC to CCDH conversion.ipynb does not currently run to completion.

needs ccdh/ccdhmodel.py to be copied in from https://github.com/cancerDHC/example-data/pull/11
needs to use string dumpers from linkml runtime

gaurav commented 3 years ago

This should be working now (as of PR #14). Could you please recheck when you have the time and make sure it's working for you? pipenv run jupyter notebook should work now.

turbomam commented 2 years ago

yes, theGDC to CCDH conversion notebook in branch main does run to completion as long as the local ccdh model is loaded as

from ccdh import ccdhmodel as ccdh

but not from PyPI with

import crdch_model.crdch_model as ccdh

I think we're all aware of this now, so I'm closing the issue.