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Make instantiation of Grounder more flexible #15

merged 4 commits into from Mar 17, 2020


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cthoyt commented Mar 16, 2020

This PR allows the user to either specify the terms_file argument to Grounder.__init__() as either a:

  • None -> look up the default path using gilda.resources.get_grounding_terms() as well as ensure the data has been downloaded from Amazon
  • str -> use the grounding terms file at the given path
  • dict -> use a pre-made dictionary of normalized names to terms, with the same structure as gilda.grounder.load_terms_file() returns

As a consequence, the redundant callings of Grounder(get_grounding_terms()) have been simplified to just Grounder().

cthoyt added 3 commits Mar 16, 2020
This allows the user to either specify terms_file as:
- None -> look up the path and download the data from Amazon if necessary (old functionality)
- str -> look up the grounding terms file at the given path
- dict -> use a pre-made dictionary of normalized names to terms
Becuase of the functionality added in the last commit, the grounding terms path is looked up automatically (using the same get_grounding_terms() function) if none is given.
@bgyori bgyori force-pushed the cthoyt:improve-api-extensibility branch from 51b7851 to 3ee07f4 Mar 17, 2020
@bgyori bgyori merged commit 3e5ff23 into indralab:master Mar 17, 2020
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@cthoyt cthoyt deleted the cthoyt:improve-api-extensibility branch Mar 17, 2020
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