Biocode FIMS

A Python client for accessing data from the Biocode FIMS database.

• Free software: MIT license
• Documentation: https://biocode-fims.readthedocs.io.

Installation

pip install biocode_fims

Basic Usage

Returning a list of all public Projects in the Biocode FIMS.

>>> import biocode_fims
>>> all_projects = biocode_fims.list_projects()
>>> print(all_projects)
{
  "Barcode of Wildlife Nigeria": 10,
  "Amphibian Disease": 26,
  "SI Barcoding CBOL": 12,
  "Hawaii Dimensions": 3,
  "University and Jepson Herbaria": 22,
  "Barcode of Wildlife Nepal": 23,
  "Barcode of Wildlife Kenya": 8,
  "New York Botanical Garden": 28,
  "Barcode of Wildlife Proficiency Testing": 24,
  "Barcode of Wildlife Mexico": 9,
  "Barcode of Wildlife South Africa": 11,
  "Barcode of Wildlife Training": 5
}

Return the first 4 datasets in the “SI Barcoding CBOL” project (project id: 12).

>>> import biocode_fims
>>> all_sibn_datasets = biocode_fims.list_datasets(12)
>>> print(all_sibn_datasets[:4])
['Brazil_Ants_A', 'Brazil_Ants_B', 'Brazil_Ants_C', 'Brazil_Ants_D']

Grab the contents of the dataset “DJBirds_P01”.

>>> import biocode_fims
>>> contents = biocode_fims.dataset_contents(12,['DJBirds_P01'])
>>> print(len(contents))
83

To do something useful with the dataset contents, it’s best of load them into a Pandas DataFrame.

TODO

• Get testing implemented correctly
• Expand to API endpoints behind OAuth

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.