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Aquarium's Python API for planning, executing, and analyzing scientific experiments.

Project description

Pydent: Aquarium API Scripting

CircleCI PyPI version

Pydent is the python API for Aquarium.

Documentation

API documentation can be found here at http://aquariumbio.github.io/pydent

Requirements

  • Python > 3.4
  • An Aquarium login

Quick installation

Pydent can be installed using pip3.

    pip3 install pydent

or upgraded using

    pip3 install pydent --upgrade

Basic Usage

Logging in

from pydent import AqSession

# open a session
mysession = AqSession("username", "password", "www.aquarium_nursery.url")

# find a user
u = mysession.User.find(1)

# print the user data
print(u)

Models

print(mysession.models)

Finding models

  • By name: nursery.SampleType.find_by_name("Primer")

  • By ID: nursery.SampleType.find(1)

  • By property: nursery.SampleType.where({'name': 'Primer'})

  • All models: nursery.SampleType.all()

Getting nested data

# samples are linked to sample_type
primer_type = mysession.SampleType.find_by_name("Primer")
primers = primer_type.samples

# and sample type is linked to sample
p = primers[0]
print(p.sample_type)

Listing Available nested relationships

primer_type = mysession.SampleType.find(1)
print(primer_type.get_relationships())

making a release

Update dependencies

poetry update
poetry build
poetry publish

To use a pypi token, the user name should be __token__ and the password should be the token including the pypi- prefix.

Update documents with make docs

Project details


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