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hubmapconsortium / hubmap-api-py-client

Python client for the Cells API
MIT License
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Mccalluc/really fix values #50

Closed mccalluc closed 3 years ago

mccalluc commented 3 years ago

This PR uses values_included the right way... but since there was only that one test that needed to be changed, I feel like our test coverage here is insufficient, but I'm also not sure what kind of values make sense to give for that parameter.

Maybe merge this as is? Or if you want to expand the tests, feel free to commit to this branch.

>>> from hubmap_api_py_client import Client, test_url
>>> client = Client(test_url)
>>> kidney_genes = client.select_genes(where='organ', has=['Kidney'], genomic_modality='rna', p_value=0.05)
>>> kidney_genes_details = kidney_genes.get_details(10)
>>> kidney_genes_details
[{'gene_symbol': 'ZNF844-1', 'go_terms': None, 'values': {}}, {'gene_symbol': 'AC025283.2', 'go_terms': None, 'values': {}}, {'gene_symbol': 'CHN2', 'go_terms': None, 'values': {}}, {'gene_symbol': 'AL358113.1', 'go_terms': None, 'values': {}}, {'gene_symbol': 'AL049629.2', 'go_terms': None, 'values': {}}, {'gene_symbol': 'ZNF670', 'go_terms': None, 'values': {}}, {'gene_symbol': 'HYDIN2', 'go_terms': None, 'values': {}}, {'gene_symbol': 'FRG1HP', 'go_terms': None, 'values': {}}, {'gene_symbol': 'CASTOR2', 'go_terms': None, 'values': {}}, {'gene_symbol': 'AL359736.1', 'go_terms': None, 'values': {}}]
>>> kidney_genes_details_w_values = kidney_genes.get_details(10, values_included=['Kidney'])
>>> kidney_genes_details_w_values
[{'gene_symbol': 'ZNF844-1', 'go_terms': None, 'values': {'Kidney': 4.867122023774583e-285}}, {'gene_symbol': 'AC025283.2', 'go_terms': None, 'values': {'Kidney': 0.0}}, {'gene_symbol': 'CHN2', 'go_terms': None, 'values': {'Kidney': 3.532389020219742e-08}}, {'gene_symbol': 'AL358113.1', 'go_terms': None, 'values': {'Kidney': 0.0}}, {'gene_symbol': 'AL049629.2', 'go_terms': None, 'values': {'Kidney': 0.0}}, {'gene_symbol': 'ZNF670', 'go_terms': None, 'values': {'Kidney': 1.3948972972658453e-68}}, {'gene_symbol': 'HYDIN2', 'go_terms': None, 'values': {'Kidney': 0.0}}, {'gene_symbol': 'FRG1HP', 'go_terms': None, 'values': {'Kidney': 0.0}}, {'gene_symbol': 'CASTOR2', 'go_terms': None, 'values': {'Kidney': 4.467999869928024e-24}}, {'gene_symbol': 'AL359736.1', 'go_terms': None, 'values': {'Kidney': 0.0}}]
SFD5311 commented 3 years ago

@mccalluc I'm writing up a few additional examples for the doc tests right now. I'll merge after that.