Skip to main content

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.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for biocode_fims, version 0.2.4
Filename, size File type Python version Upload date Hashes
Filename, size biocode_fims-0.2.4-py2.py3-none-any.whl (6.5 kB) File type Wheel Python version py2.py3 Upload date Hashes View
Filename, size biocode_fims-0.2.4.tar.gz (14.6 kB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page