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_fimsBasic 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))
83If you would like to have these contents returned in the form of a Pandas DataFrame, add the option format='dataframe'. By default, the DataFrame will be returned pre-sorted by 'extractionPlateID', and then 'extractionWell'.
>>> import biocode_fims
>>> fims_df = biocode_fims.dataset_contents(12, ['DJBirds_P01'], format='dataframe')
>>> print(fims_df[['extractionPlateID','extractionWell','voucherID','scientificName']].head())| Â | extractionPlateID | extractionWell | voucherID | scientificName |
|---|---|---|---|---|
| 40 | DJBirds01 | A01 | USNM:Birds:647764 | Threskiornis aethiopicus |
| 11 | DJBirds01 | B01 | USNM:Birds:647765 | Corvus splendens |
| 12 | DJBirds01 | C01 | USNM:Birds:647766 | Threskiornis aethiopicus |
| 0 | DJBirds01 | D01 | USNM:Birds:647762 | Dromas ardeola |
| 13 | DJBirds01 | E01 | USNM:Birds:647767 | Dromas ardeola |
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.
