============
Biocode FIMS
============
.. image:: https://img.shields.io/pypi/v/biocode_fims.svg
:target: https://pypi.python.org/pypi/biocode_fims
.. image:: https://img.shields.io/travis/MikeTrizna/biocode_fims.svg
:target: https://travis-ci.org/MikeTrizna/biocode_fims
.. image:: https://readthedocs.org/projects/biocode-fims/badge/?version=latest
:target: https://biocode-fims.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
.. image:: https://pyup.io/repos/github/MikeTrizna/biocode_fims/shield.svg
:target: https://pyup.io/repos/github/MikeTrizna/biocode_fims/
:alt: Updates
A Python client for accessing data from the `Biocode FIMS <http://www.biscicol.org/>`_ database.
* Free software: MIT license
* Documentation: https://biocode-fims.readthedocs.io.
Installation
------------
.. code-block:: python
pip install biocode_fims
Basic Usage
-----------
Returning a list of all *public* Projects in the Biocode FIMS.
.. code-block:: python
>>> 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).
.. code-block:: python
>>> 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".
.. code-block:: python
>>> 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.
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
=======
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.
