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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