ohsu-comp-bio / g2p-aggregator

Associations of genomic features, drugs and diseases

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Cannot use disease_normalizer without setting BIOONTOLOGY_API_KEY

prismofeverything opened this issue · comments

When trying to import harvester/disease_normalizer.py I get the following error:

In [1]: import disease_normalizer
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-1-d4ae6bedd91b> in <module>()
----> 1 import disease_normalizer

/Users/rspangler/Code/g2p-aggregator/harvester/disease_normalizer.py in <module>()
     11 API_KEY = os.environ.get('BIOONTOLOGY_API_KEY')
     12 if not API_KEY:
---> 13     raise ValueError('Please set BIOONTOLOGY_API_KEY in environment')
     14 
     15 

ValueError: Please set BIOONTOLOGY_API_KEY in environment

It would be ideal if the tool could be used even if I don't have a BIOONTOLOGY_API_KEY, as the code uses other sources to find matches as well.