A library designed to simplify various research tasks for users looking to leverage the NMDC (National Microbiome Data Collaborative) APIs. The library provides a collection of general-purpose functions that facilitate easy access, manipulation, and analysis of microbiome data.
Until this available through pip, the best usage will be to clone the repo and use like this example:
from nmdc_notebook_tools.collection import Collection
# Create an instance of the module
collection_client = Collection()
# Use the variable to call the available functions
collection_client.get_collection_by_id("biosample", "id")I would recommend periodically runnning git pull to get the latest updates.
To see debugging information, include these two lines where ever you are running the functions:
import logging
logging.basicConfig(level=logging.DEBUG)
# when this is run, you will see debug information in the console.
collection_client.get_collection_by_id("biosample", "id")Note: nmdc_notebook_tools will eventually be available at pip install nmdc_notebook_tools but is still in development.
Documentation about available functions and helpful usage notes can be found at https://microbiomedata.github.io/nmdc_notebook_tools/.