pydent 0.0.27

Aquarium scripting

CircleCI PyPI version

Trident is the python API scripting for Aquarium.

1. Installation - how to install pydent

2. Examples - example usages

3. Contributing - contributing and developer notes

4. API Notes - notes on pydent/Aquarium models

5. Tests - testing notes

Note: the initial version is tagged as v0.0.1-initial, but is no longer being developed.

Documentation

API documentation can be found here at klavinslab.org/trident

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)

Available nested relationships

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