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.