pyobis

Python client for the OBIS API.

Source on GitHub at iobis/pyobis

For examples of how to use this repo, see the jupyter notebooks in the /notebooks/ directory. NOTE: GitHub's jupyter notebook display does not show interactive plots; open the notebooks in a jupyter hub (eg colab, binder, etc) for the full experience.

Other OBIS clients:

• R: robis, iobis/robis

Installation

Install from pypi

pip install pyobis

Install latest dev version from github

pip install git+git://github.com/sckott/pyobis.git#egg=pyobis

Install editable dev version from github for local development. System prerequisites: python3, conda

# fetch code
git clone [email protected]:iobis/pyobis.git
cd pyobis
# install
python -m pip install -r requirements.txt
python -m pip install -r requirements-dev.txt
python -m pip install -e .
# test your installation
python -m pytest

Library API

pyobis is split up into modules for each of the groups of API methods.

• taxa - Taxonomic names
• occurrences - Occurrence search
• dataset - Dataset
• nodes - Nodes
• checklist - Checklist

You can import the entire library, or each module individually as needed.

Taxa module

from pyobis import taxa
taxa.search(scientificname = 'Mola mola')
taxa.search(scientificname = 'Mola mola', offset=10, limit=10)
taxa.search(geometry='POLYGON((30.1 10.1, 10 20, 20 40, 40 40, 30.1 10.1))', limit=20)
taxa.search(aphiaid=key, year="2013", limit=20)
taxa.taxon(406296)
taxa.taxon(415282)

Occurrence module

Search

from pyobis import occurrences
occurrences.search(scientificname = 'Mola mola')
occurrences.search(scientificname = 'Mola mola', offset=0, limit=10)
occurrences.search(geometry='POLYGON((30.1 10.1, 10 20, 20 40, 40 40, 30.1 10.1))', limit=20)
occurrences.search(aphiaid=key, year="2013", limit=20)

Download

res = occ.download(year = 2001, scientificname = 'Orcinus')
res.uuid
res.status()
res.fetch()

Dataset module

from pyobis import dataset
dataset.search(scientificname = ['Mola', 'Abra', 'Lanice', 'Pectinaria'])
dataset.get(id = 'ec9df3b9-3b2b-4d83-881b-27bcbcd57b95')

Nodes module

from pyobis import nodes
nodes.search(scientificname = ['Mola', 'Abra'] )

Checklist module

from pyobis import checklist as ch
ch.list(year = 2005, scientificname = 'Cetacea')

Meta

• License: MIT, see LICENSE file
• Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.