A Python client for accessing data from the Biocode FIMS database.
Project description
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.
History
0.2.0 (2017-06-29)
Changed dataset_contents function to filter out empty fields by default
Got documentation running on RTD, and continuous integration running on TravisCI
0.1.0 (2017-06-21)
Initial release on PyPI.
Project details
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