Aquarium's Python API for planning, executing, and analyzing scientific experiments.
Project description
Trident: Aquarium API Scripting
Trident is the python API scripting for Aquarium.
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)
Project details
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