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

Project description

Biocode FIMS Documentation Status Updates

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


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))

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


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


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


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.

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